https://sourceforge.net/p/reditools/activity/Recent activity for reditoolsenTue, 30 Jul 2019 02:26:40 -0000https://sourceforge.net/p/reditools/tickets/12/?limit=25#ac7fDear Ernesto, I am using REDItools 1.2.1 (Pysam 0.15.2). Once I start REDItoolDnaRna.py, I also have the above problem, described as follows. I want to know what caused this error and how to fix it. Could you please have a look at this problem and help me out. Thank you very much! Best wishes, Sijia python /home/binfo/RNAediting/software/installpath/bin/REDItoolDnaRna.py -i rna.bam -j dna.bam -f reference.fa -o /home/binfo/RNAediting/sampledata/output/ -c 10,1 -q 25,25 -m 20,20 -s 2 -g 1 -u -a 6-0...Sijia WuTue, 30 Jul 2019 02:26:40 -0000https://sourceforge.net/p/reditools/tickets/12/?limit=25#ac7fhttps://sourceforge.net/p/reditools/tickets/12/?limit=25#ae77Dear Chris, thank you for reporting this issue. The bug due to the use of an old pysam function has been fixed. A novel version is now available, 1.2.1 Best, Ernesto Il giorno 8 apr 2019, alle ore 18:28, ChrisAI chria-ai@users.sourceforge.net ha scritto: [tickets:#12] https://sourceforge.net/p/reditools/tickets/12/ TypeError: ord() expected string of length 1, but int found Status: New Created: Mon Apr 08, 2019 04:28 PM UTC by ChrisAI Last Updated: Mon Apr 08, 2019 04:28 PM UTC Owner: nobody Dear...Ernesto PicardiWed, 17 Apr 2019 09:48:09 -0000https://sourceforge.net/p/reditools/tickets/12/?limit=25#ae77https://sourceforge.nethttps%3A//sourceforge.net/projects/reditools/files/REDItools-1.2.1.zip/downloadreditoolsWed, 17 Apr 2019 09:20:02 -0000https://sourceforge.net/projects/reditools/files/REDItools-1.2.1.zip/downloadhttps://sourceforge.net/p/reditools/tickets/12/TypeError: ord() expected string of length 1, but int foundChrisAIMon, 08 Apr 2019 16:28:51 -0000https://sourceforge.net/p/reditools/tickets/12/https://sourceforge.nethttps%3A//sourceforge.net/projects/reditools/files/REDItools-1.2.tar.gz/downloadreditoolsThu, 20 Dec 2018 22:19:02 -0000https://sourceforge.net/projects/reditools/files/REDItools-1.2.tar.gz/downloadhttps://sourceforge.net/p/reditools/tickets/11/Get reditools merged result, but not all scaffoldsLiuxiangMon, 17 Dec 2018 07:59:32 -0000https://sourceforge.net/p/reditools/tickets/11/https://sourceforge.net/p/reditools/tickets/10/?limit=25#2be6Dear Ernesto, I’ve tried what you pointed out on your last response. I got back the pysam 0.13 and tried to run the REDItoolDnaRna_1.1.py you provided me with last time. Unfortunately it doesn’t work again. My input is: python REDItoolDnaRna_1.1.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam \ -I /Users/tasakis/Documents/Moor_BAM/SortedBAMs/SRR5280291Aligned.sortedByCoord.out.bam \ -f /Users/tasakis/Documents/Mus_musculus.GRCm38.dna_sm.toplevel.fa \ -o /Users/tasakis/Desktop/TEST...Rafail TasakisThu, 04 Jan 2018 13:11:21 -0000https://sourceforge.net/p/reditools/tickets/10/?limit=25#2be6https://sourceforge.net/p/reditools/tickets/10/?limit=25#cffb/c390Dear Rafail, pysam version may be an issue. Please use the attached version instead. It is based on the latest pysam release. Let me know if it works. Best, Ernesto Il giorno 13 dic 2017, alle ore 11:14, Rafail Tasakis tasakis@users.sf.net ha scritto: Dear Ernesto, thank you very much for getting back to me. I tried as you said. Also made sure that the fa.fai file of the reference genome is in the same directory with that. My input command it this now: REDItoolDnaRna.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam...Ernesto PicardiWed, 13 Dec 2017 10:24:48 -0000https://sourceforge.net/p/reditools/tickets/10/?limit=25#cffb/c390https://sourceforge.net/p/reditools/tickets/10/?limit=25#cffbDear Ernesto, thank you very much for getting back to me. I tried as you said. Also made sure that the fa.fai file of the reference genome is in the same directory with that. My input command it this now: REDItoolDnaRna.py -i /Users/tasakis/Documents/Moor_BAM/UnsortedBAMs/SRR5280291Aligned.out.bam \ -I /Users/tasakis/Documents/Moor_BAM/SortedBAMs/SRR5280291Aligned.sortedByCoord.out.bam \ -f /Users/tasakis/Documents/mm10.fa \ -o /Users/tasakis/Desktop/TEST -F RUN However I still ge the same error....Rafail TasakisWed, 13 Dec 2017 10:14:43 -0000https://sourceforge.net/p/reditools/tickets/10/?limit=25#cffbhttps://sourceforge.net/p/reditools/tickets/10/?limit=25#7d29Dear Rafail, there is an error in your command line. -F option requires a string to create a directory inside the output folder. you should try using: -o /Users/tasakis/Desktop/TEST -F RUN This will create a TEST folder and inside a nested RUN folder containing results. Regarding the genome fasta file, is it indexed? So, please check the presence of /Users/tasakis/Documents/mm10.fa.fai file. Otherwise please run this command before: samtools faidx /Users/tasakis/Documents/mm10.fa For more details,...Ernesto PicardiWed, 13 Dec 2017 08:09:34 -0000https://sourceforge.net/p/reditools/tickets/10/?limit=25#7d29https://sourceforge.net/p/reditools/tickets/10/Fasta file not found, while I provide itRafail TasakisTue, 12 Dec 2017 17:49:25 -0000https://sourceforge.net/p/reditools/tickets/10/https://sourceforge.net/p/reditools/tickets/9/?limit=25#5a70Hi, my impression is that pysam version is not corrected. You should use version 0.6 or 0.7. Best, Ernesto Il giorno 01 nov 2017, alle ore 13:25, wangzhennan wangzhennan@users.sf.net ha scritto: [tickets:#9] https://sourceforge.net/p/reditools/tickets/9/ list index out of range Status: New Created: Wed Nov 01, 2017 12:25 PM UTC by wangzhennan Last Updated: Wed Nov 01, 2017 12:25 PM UTC Owner: nobody HI, When I used REDItools to deal with my data, there is an error: Script time --> START: 01/11/2017...Ernesto PicardiFri, 03 Nov 2017 08:34:16 -0000https://sourceforge.net/p/reditools/tickets/9/?limit=25#5a70https://sourceforge.net/p/reditools/tickets/9/ list index out of rangewangzhennanWed, 01 Nov 2017 12:25:41 -0000https://sourceforge.net/p/reditools/tickets/9/https://sourceforge.net/p/reditools/tickets/8/?limit=25#71a6Hi, many thanks for your work! I may ask people in our group to do some tests...and...Ernesto PicardiTue, 30 Aug 2016 15:34:25 -0000https://sourceforge.net/p/reditools/tickets/8/?limit=25#71a6https://sourceforge.net/p/reditools/tickets/8/Update to pysamAMCTue, 23 Aug 2016 03:57:38 -0000https://sourceforge.net/p/reditools/tickets/8/https://sourceforge.net/p/reditools/tickets/7/?limit=25#6f8cHi rivaldotry, sorry for the delay. You are correct. The OutSub file prints out the...Ernesto PicardiWed, 08 Jun 2016 14:43:02 -0000https://sourceforge.net/p/reditools/tickets/7/?limit=25#6f8chttps://sourceforge.net/p/reditools/tickets/7/a question about the output file of REDItoolDenovorivaldotryWed, 25 May 2016 17:16:42 -0000https://sourceforge.net/p/reditools/tickets/7/https://sourceforge.net/p/reditools/tickets/6/?limit=25#e3a2Dear Stéphanie, sorry for the inconvenient. The documentation is now available at...Ernesto PicardiFri, 29 Apr 2016 09:48:07 -0000https://sourceforge.net/p/reditools/tickets/6/?limit=25#e3a2https://sourceforge.net/p/reditools/tickets/6/List example of known RNA editing events for REDItoolKnown.pyStéphanieThu, 28 Apr 2016 08:42:43 -0000https://sourceforge.net/p/reditools/tickets/6/https://sourceforge.net/p/reditools/tickets/5/?limit=25#78b3/7360Hi Using 0.7.4 works fine. Please try also one of 0.6.x I'm working to fix pysam...Ernesto PicardiFri, 12 Feb 2016 13:33:30 -0000https://sourceforge.net/p/reditools/tickets/5/?limit=25#78b3/7360https://sourceforge.net/p/reditools/tickets/5/?limit=250#78b3HI, thanks for your answer. I unistalled pysam and I returned to install pysam 0.7.5....antonioFri, 12 Feb 2016 09:15:48 -0000https://sourceforge.net/p/reditools/tickets/5/?limit=250#78b3https://sourceforge.net/p/reditools/tickets/5/?limit=25#bbe9Hi, the error is in the pysam version. You should use 0.6 or 0.7. Best, Ernesto Il...Ernesto PicardiWed, 10 Feb 2016 16:54:41 -0000https://sourceforge.net/p/reditools/tickets/5/?limit=25#bbe9https://sourceforge.net/p/reditools/tickets/5/Error in REDItoolDnaRna.pyantonioWed, 10 Feb 2016 11:27:01 -0000https://sourceforge.net/p/reditools/tickets/5/https://sourceforge.nethttp%3A//sourceforge.net/projects/reditools/files/README/downloadreditoolsMon, 23 Feb 2015 13:18:03 -0000http://sourceforge.net/projects/reditools/files/README/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/reditools/files/index.rst/downloadreditoolsMon, 23 Feb 2015 13:15:04 -0000http://sourceforge.net/projects/reditools/files/index.rst/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/reditools/files/REDItools-1.0.4.tar.gz/downloadreditoolsMon, 23 Feb 2015 12:54:03 -0000http://sourceforge.net/projects/reditools/files/REDItools-1.0.4.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/reditools/files/REDItools-1.0.tar.gz/downloadreditoolsMon, 23 Feb 2015 09:31:02 -0000http://sourceforge.net/projects/reditools/files/REDItools-1.0.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/reditools/files/REDItools-1.0.2.tar.gz/downloadreditoolsMon, 23 Feb 2015 09:31:02 -0000http://sourceforge.net/projects/reditools/files/REDItools-1.0.2.tar.gz/downloadhttps://sourceforge.nethttp%3A//sourceforge.net/projects/reditools/files/REDItools-1.0.3.tar.gz/downloadreditoolsMon, 23 Feb 2015 09:31:02 -0000http://sourceforge.net/projects/reditools/files/REDItools-1.0.3.tar.gz/downloadhttps://sourceforge.net/p/reditools/files/Ernesto PicardiMon, 23 Feb 2015 09:29:22 -0000https://sourceforge.net/p/reditools/files/https://sourceforge.net/p/reditools/tickets/Ernesto PicardiMon, 23 Feb 2015 09:28:52 -0000https://sourceforge.net/p/reditools/tickets/https://sourceforge.net/p/reditools/code/Ernesto PicardiMon, 23 Feb 2015 09:28:50 -0000https://sourceforge.net/p/reditools/code/