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huyustats / SCATS

A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
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Error quantification set #10

Open TdzBAS opened 1 year ago

TdzBAS commented 1 year ago

when i want to execute the bash scripts for quantification it fails due to an empty dictionary, which is compared with an integertype. How can i fix this? Hope someone has an Idea.

image

huyustats commented 1 year ago

Hi,

One possible reason is that the starting position of the reads is not a valid number. Please check the mapping quality of each read.

Thanks!

TdzBAS commented 1 year ago

Hi,

thanks for the response! I filtered bam file with samtools, where i exclueded reads that failed platform/vendor quality checks (512) and reads that are PCR or optical duplicates (0x400).

Do you recommend other filtering steps (unmapped reads, mates)? how would you check the ammping quality of each read?

Thanks!

huyustats commented 1 year ago

Hi,

Is the filtered bam file working now?

TdzBAS commented 1 year ago

No, unfortunately not.. I also did a quality filtering with the threshold 20. command was: "samtools view -q 30 -b -F 1540 {input} -o {output}"

The BAM file is created with aligning simulated reads generated from Polyester to GRCh37.p13 referencegenome via STAR.

When i do the filtering with the above command, I actually get the same BAM File. And therefore still the same error message.

Cheers

huyustats commented 1 year ago

I will check the code and start to do debug. Thanks

No, unfortunately not.. I also did a quality filtering with the threshold 20. command was: "samtools view -q 30 -b -F 1540 {input} -o {output}"

The BAM file is created with aligning simulated reads generated from Polyester to GRCh37.p13 referencegenome via STAR.

When i do the filtering with the above command, I actually get the same BAM File. And therefore still the same error message.

Cheers

TdzBAS commented 1 year ago

Thanks! that would be really helpful! I am rally interested in getting it running..

maybe an extra info: for this sample, the error occurs because of readStart[readName[2]]. this is the empty diictionary. For the other replicates/sample I didnt check it which variable was causing the error. Maybe this helps.

Looking really forward!

TdzBAS commented 1 year ago

@huyustats could solve the problem, after doing a qualitycontrol of the bam files. But this part works now!