Ernesto Picardi

Dear 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...

Dear 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...

Dear 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,...

Hi, 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...

Hi, many thanks for your work! I may ask people in our group to do some tests...and...

Hi rivaldotry, sorry for the delay. You are correct. The OutSub file prints out the...

Dear Stéphanie, sorry for the inconvenient. The documentation is now available at...

Hi Using 0.7.4 works fine. Please try also one of 0.6.x I'm working to fix pysam...