search

natsuhiko / rasqual

Robust Allele Specific Quantification and quality controL
37 stars 20 forks source link

Wrong number of fSNPs using helper scripts #51

Closed liesaweigert closed 3 years ago

liesaweigert commented 3 years ago

Hey, I am currently using rasqual with the helper tools from kauralasoo on some ATAC data and a lot of my peaks get skipped with this message: The number of fSNPs is greater than that specified by '-m' option. Aborted... Since the -m option is calculated by the helper script, I was wondering if there are any common mistakes or special things I should look out for.

natsuhiko commented 3 years ago

Hi,

I cannot tell you the trick to modify the rasqualtool, but it looks your input has some issue. Can you paste the actual rasqual command with the feature start position, the feature end position and the number of SNPs within the feature?

Best regards, Natsuhiko

liesaweigert commented 3 years ago

Hey, thank you so much for the answer, here are some examples for the commands. tabix VCF_files/GSA_LMU_DEC2020_ATAC_AS.vcf.gz 1:53808893-54209514 | /psycl/g/mpsziller/rasqual/bin/rasqual -y ATAC_out/ATAC.features.final.bin -k ATAC_out/ATAC.offset.final.bin -n 83 -j 3163 -f 1:54008893:54009514 -l 1323 -m 1 -s 54008893 -e 54009514 -z --force --n-threads 16 --w 2e5 -r -x ATAC_out/ATAC.covariates.bin >> output_ATAC/atac_out.final.perm.batch98.txt tabix VCF_files/GSA_LMU_DEC2020_ATAC_AS.vcf.gz 1:53811620-54212103 | /psycl/g/mpsziller/rasqual/bin/rasqual -y ATAC_out/ATAC.features.final.bin -k ATAC_out/ATAC.offset.final.bin -n 83 -j 3164 -f 1:54011620:54012103 -l 1324 -m 3 -s 54011620 -e 54012103 -z --force --n-threads 16 --w 2e5 -r -x ATAC_out/ATAC.covariates.bin >> output_ATAC/atac_out.final.perm.batch98.txt

natsuhiko commented 3 years ago

What is the output for

tabix VCF_files/GSA_LMU_DEC2020_ATAC_AS.vcf.gz 1:54008893-54009514 | wc -l

?

liesaweigert commented 3 years ago

The output for the command is 4, and is consistently bigger than the inputs I give them. My problem is that I am computing them using the rasqualTools and I don't know why it's not working correctly or if there is another way to calculate the fSNPs for multiple inputs.

natsuhiko commented 3 years ago

Unfortunately I cannot really handle the issue. Please ask Kaur for further help.

Best regards, Natsuhiko

kauralasoo commented 3 years ago

Yes, I was the person who originally wrote rasqualTools, but I haven't touched to code in the past 5 years and I am unable to maintain it. You might be better off preparing the input files for rasqual manually.

Zepeng-Mu commented 3 years ago

@liesaweigert Did you update GSA_LMU_DEC2020_ATAC_AS.vcf.gz after running rasqualTools? I made this error when I was running rasqual