Sijia Wu posted a comment on ticket #12

Dear 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...

Ernesto Picardi posted a comment on ticket #12

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...

reditools released /REDItools-1.2.1.zip

ChrisAI created ticket #12

TypeError: ord() expected string of length 1, but int found

reditools released /REDItools-1.2.tar.gz

Liuxiang created ticket #11

Get reditools merged result, but not all scaffolds

Rafail Tasakis posted a comment on ticket #10

Dear 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...

Ernesto Picardi posted a comment on ticket #10

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...

Rafail Tasakis posted a comment on ticket #10

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 \ -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....

Ernesto Picardi posted a comment on ticket #10

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,...

Rafail Tasakis created ticket #10

Fasta file not found, while I provide it

Ernesto Picardi posted a comment on ticket #9

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...

wangzhennan created ticket #9

list index out of range

Ernesto Picardi posted a comment on ticket #8

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

AMC created ticket #8

Update to pysam

Ernesto Picardi posted a comment on ticket #7

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

rivaldotry created ticket #7

a question about the output file of REDItoolDenovo

Ernesto Picardi posted a comment on ticket #6

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

Stéphanie created ticket #6

List example of known RNA editing events for REDItoolKnown.py

Ernesto Picardi posted a comment on ticket #5

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

antonio posted a comment on ticket #5

HI, thanks for your answer. I unistalled pysam and I returned to install pysam 0.7.5....

Ernesto Picardi posted a comment on ticket #5

Hi, the error is in the pysam version. You should use 0.6 or 0.7. Best, Ernesto Il...

antonio created ticket #5

Error in REDItoolDnaRna.py

reditools released /README

reditools released /index.rst

reditools released /REDItools-1.0.4.tar.gz

reditools released /REDItools-1.0.tar.gz

reditools released /REDItools-1.0.2.tar.gz

reditools released /REDItools-1.0.3.tar.gz

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