https://sourceforge.net/p/ppline/activity/Recent activity for PPLineenMon, 26 Mar 2018 17:26:04 -0000https://sourceforge.nethttps%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.9.tar.gz/downloadPPLineMon, 26 Mar 2018 17:26:04 -0000https://sourceforge.net/projects/ppline/files/PPLine.0.9.9.tar.gz/downloadhttps://sourceforge.nethttps%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.8.5.tar.gz/downloadPPLineThu, 11 Jan 2018 09:17:03 -0000https://sourceforge.net/projects/ppline/files/PPLine.0.9.8.5.tar.gz/downloadhttps://sourceforge.nethttps%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.8.4.with.preinstalled.soft.tar.gz/downloadPPLineSun, 12 Jun 2016 21:24:04 -0000https://sourceforge.net/projects/ppline/files/PPLine.0.9.8.4.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttps%3A//sourceforge.net/projects/ppline/files/README.md/downloadPPLineSun, 12 Jun 2016 11:09:03 -0000https://sourceforge.net/projects/ppline/files/README.md/downloadhttps://sourceforge.nethttps%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.8.3.with.preinstalled.soft.tar.gz/downloadPPLineWed, 16 Mar 2016 17:32:02 -0000https://sourceforge.net/projects/ppline/files/PPLine.0.9.8.3.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.8.2.with.preinstalled.soft.tar.gz/downloadPPLineSun, 07 Feb 2016 06:10:03 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.8.2.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#c8e21) No, Tophat-fusion is not a part of PPline. I strongly recommend deFuse as it is...gskrasnovThu, 10 Dec 2015 08:11:42 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#c8e2https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#2a58Thank You for the great work! My Ppline run has just finished succesfully! I have...avkitexSun, 06 Dec 2015 13:11:16 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#2a58https://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/ppline.0.9.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/ppline.0.9.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.8.with.preinstalled.soft.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.8.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.5.with.preinstalled.soft.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.5.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/ppline.0.9.1.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/ppline.0.9.1.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.3.with.preinstalled.soft.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.3.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.7.with.preinstalled.soft.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.7.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.6.with.preinstalled.soft.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.6.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.4.with.preinstalled.soft.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.4.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.3.tar.gz/downloadPPLineThu, 03 Dec 2015 11:56:03 -0000http://sourceforge.net/projects/ppline/files/Old.releases/PPLine.0.9.3.tar.gz/downloadhttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#61edPPLIne 0.9.8.1 is releleased - Ppline automatically downloads all the database at...gskrasnovThu, 03 Dec 2015 08:05:13 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#61edhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.8.1.with.preinstalled.soft.tar.gz/downloadPPLineThu, 03 Dec 2015 07:54:02 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.8.1.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.8.1.tar.gz/downloadPPLineThu, 03 Dec 2015 07:40:02 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.8.1.tar.gz/downloadhttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#44a1I will add the quality rescoring feature in the next release (when i'll have time...gskrasnovTue, 01 Dec 2015 12:45:31 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#44a1https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#5ca9I'm not familiar with GATK. I am testing PPline on SRR1609982. I believe that it...Nikita KotlovMon, 30 Nov 2015 14:05:54 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#5ca9https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#334aYes, that's a really good idea. I'll try PPLine on a clean Ubuntu VM to uncover the...gskrasnovTue, 24 Nov 2015 09:10:53 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#334ahttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#fe2eThank you for the improovements. I'm running PPline on Ubuntu 14 (on rackspace) I'll...Nikita KotlovTue, 24 Nov 2015 07:00:27 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#fe2ehttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#43dcAlso it would be great idea to have some "steps" of the pipeline running. It means...Nikita KotlovTue, 24 Nov 2015 06:28:46 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#43dchttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#fe2eThank you for the improovements. I'm running PPline on Ubuntu 14 (on rackspace) I'll...Nikita KotlovMon, 23 Nov 2015 20:21:37 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#fe2ehttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#930eTopHat uses system bowtie2 instead of the one located in Useful.stuf/ dir [2015-11-21...Nikita KotlovMon, 23 Nov 2015 20:11:00 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#930ehttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#930eTopHat uses system bowtie2 instead of the one located in Useful.stuf/ dir [2015-11-21...Nikita KotlovMon, 23 Nov 2015 20:10:58 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#930ehttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/README/downloadPPLineMon, 23 Nov 2015 09:12:02 -0000http://sourceforge.net/projects/ppline/files/README/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.8.with.preinstalled.soft.tar.gz/downloadPPLineMon, 23 Nov 2015 09:11:02 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.8.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#0c81Dear Nikita, Thank you for the bug report! I have fixed all the mentioned bugz except...gskrasnovMon, 23 Nov 2015 09:10:24 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#0c81https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#930eTopHat uses system bowtie2 instead of the one located in Useful.stuf/ dir [2015-11-21...Nikita KotlovSun, 22 Nov 2015 14:11:37 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#930ehttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#8e1dit is needed to install HTSeq-0.6.1 https://pypi.python.org/pypi/HTSeq and specify...Nikita KotlovThu, 12 Nov 2015 12:37:40 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#8e1dhttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#2fcbDuring vcf file reordering perl script consumed more than 57 Gb of memory and finally...Nikita KotlovWed, 04 Nov 2015 09:01:50 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#2fcbhttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#ec10And by the way there is no link to dbSNP database: ftp://ftp.ncbi.nih.gov/snp/organisms/...Nikita KotlovTue, 03 Nov 2015 14:18:17 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#ec10https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#094eDear authors, I'm fond of your pipeline. Im going to report all detected bugs in...Nikita KotlovTue, 03 Nov 2015 09:18:46 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#094ehttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#094eDear authors, I'm fond of your pipeline. Im going to report all detected bugs in...Nikita KotlovTue, 03 Nov 2015 09:18:31 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#094ehttps://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#094eDear authors, I'm fond of your pipeline. Im going to report all detected bugs in...Nikita KotlovTue, 03 Nov 2015 09:17:07 -0000https://sourceforge.net/p/ppline/discussion/general/thread/41a53596/?limit=25#094ehttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.7.with.preinstalled.soft.tar.gz/downloadPPLineSat, 17 Oct 2015 09:35:03 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.7.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/README/downloadPPLineSat, 17 Oct 2015 09:26:03 -0000http://sourceforge.net/projects/ppline/files/README/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.6.with.preinstalled.soft.tar.gz/downloadPPLineFri, 25 Sep 2015 11:12:04 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.6.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.5.with.preinstalled.soft.tar.gz/downloadPPLineThu, 20 Aug 2015 20:49:02 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.5.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.4.with.preinstalled.soft.tar.gz/downloadPPLineWed, 05 Aug 2015 12:37:03 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.4.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.3.with.preinstalled.soft.tar.gz/downloadPPLineSun, 07 Jun 2015 15:06:05 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.3.with.preinstalled.soft.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine.0.9.3.tar.gz/downloadPPLineSun, 07 Jun 2015 15:06:05 -0000http://sourceforge.net/projects/ppline/files/PPLine.0.9.3.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Sample.Output.Results/Alt.and.Ref.Proteins.fasta.tar.gz/downloadPPLineSun, 07 Jun 2015 14:53:02 -0000http://sourceforge.net/projects/ppline/files/Sample.Output.Results/Alt.and.Ref.Proteins.fasta.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Sample.Output.Results/SNP.SAP.table.xlsx/downloadPPLineSun, 07 Jun 2015 14:44:02 -0000http://sourceforge.net/projects/ppline/files/Sample.Output.Results/SNP.SAP.table.xlsx/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/Sample.Output.Results/Novel.splice.forms.chr18.xlsx/downloadPPLineSun, 07 Jun 2015 14:43:02 -0000http://sourceforge.net/projects/ppline/files/Sample.Output.Results/Novel.splice.forms.chr18.xlsx/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/ppline.0.9.1.tar.gz/downloadPPLineFri, 05 Jun 2015 10:58:02 -0000http://sourceforge.net/projects/ppline/files/ppline.0.9.1.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/ppline.0.9.tar.gz/downloadPPLineThu, 04 Jun 2015 19:36:05 -0000http://sourceforge.net/projects/ppline/files/ppline.0.9.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/README/downloadPPLineThu, 04 Jun 2015 19:27:04 -0000http://sourceforge.net/projects/ppline/files/README/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine_Getting_started_and_Manual.pdf/downloadPPLineThu, 04 Jun 2015 19:27:04 -0000http://sourceforge.net/projects/ppline/files/PPLine_Getting_started_and_Manual.pdf/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/README.txt/downloadPPLineThu, 04 Jun 2015 19:24:02 -0000http://sourceforge.net/projects/ppline/files/README.txt/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/PPLine_Getting_started_and_Manual.pdf/downloadPPLineThu, 04 Jun 2015 19:24:02 -0000http://sourceforge.net/projects/ppline/files/PPLine_Getting_started_and_Manual.pdf/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/README/downloadPPLineThu, 28 May 2015 23:05:03 -0000http://sourceforge.net/projects/ppline/files/README/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/ppline/files/ppline.pre.release.0.8.tar.gz/downloadPPLineThu, 28 May 2015 22:52:03 -0000http://sourceforge.net/projects/ppline/files/ppline.pre.release.0.8.tar.gz/download