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MIAOKUI / PSI

PSI calculation script
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PSI.sh run error #2

Open skytguuu opened 4 years ago

skytguuu commented 4 years ago

Hi,

Recently, I tried to use your developed tool "PSI" to calculate psi. Firstly, I got the output from STAR software, then I used the command to transfor SJ.out.tab file into junction file: ############## awk 'BEGIN{OFS="\t"}{print $1, $2-20-1, $3+20, "JUNCBJ"NR, $7, ($4 == 1)? "+":"‐",$2-20-1, $3+20, "255,0,0", 2, "20,20", "0,300" }' SJ.out.tab > junctions.bed ############## Next, I have transfer the gtf with DXESeq software then use the command to call psi: ############## bash psi_shell/PSI_v2.0 StartPSIStrictFiltergecode_mm9.gff 150 Aligned_sort.out.bam junctions.bed test ############## However, it failed with the error that: ############

Counting exon coverage.... ***** WARNING: File ../Aligned.out.bam has inconsistent naming convention for record: NT_166308 40435 40561 SRR2927026.7744/2 3 + ############# I have check the junction bed and gft file, the chromosome names are all "chr". So, I don't know what's happened? Could you give me a hand?

Thanks! Best

DerSeb81 commented 4 years ago

Hello,

There is a problem with the bedtools version. They switched the -a and -b arguments. Try to use bedtols version from 2015 or change the code for intersectbed in your script.

cheers, seb