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PSI-Sigma
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long reads RNA-seq dataset #19

Closed JamalEH closed 3 years ago

JamalEH commented 3 years ago

Dear Woody,

I have a Nanopore long reads RNA-seq dataset on which I want to run PSIsigma. The output from PSIsigma contains only IR events in the *.sorted output file. I precise that I have only one single sample per groub (groupa.txt 1 sample and groupb.txt 1 sample).

Used commands: /minimap2-2.17/minimap2 -ax splice:hq -uf H38.fa MinION_long_read.fastq > .sam samtools view -bS .sam > .bam samtools sort .bam -o .Aligned.sortedByCoord.out.bam samtools index .Aligned.sortedByCoord.out.bam

PSIsigma: perl ~/PSIsigma/dummyai.pl --gtf Homo_sapiens.GRCh38.87.sorted.gtf --name PSIsigma --type 2 -nread 10

While the .IR files were generated properly, the .SJ files were empty.

I will be thankful if you could help me understand this issue and why only getting IR events in PSI sigma output file !

Kind regards, Jamal.

wososa commented 3 years ago

Hi @JamalEH,

To generate .SJ.out.tab files, you will need to have "awk" command. You can try the following command:

samtools view A1.bam | awk -f ~/PSIsigma/sjFromSAMcollapseUandM_inclOverlaps.awk > A1.SJ.out.tab

Cheers, Woody

JamalEH commented 3 years ago

Dear Woody,

I tried to run the above-mentioned function but it generates empty "*.SJ.out.tab", just like what it happens with the main function of PSIsigma.

Should I re-run the alignment step using minimap2?

Thank you in advance! Best regards, Jamal.

wososa commented 3 years ago

Hi @JamalEH ,

You probably should use minimap2 to generate the .bam file again. Unless your system doesn't have awk or samtools installed.

Cheers, Woody