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No reads in Output of MMARGE.pl allele_specific_reads #8

Closed njwehi closed 2 weeks ago

njwehi commented 5 months ago

Hi,

I found No reads in Output of MMARGE.pl allele_specific_reads

samtools view

it was data from F1 mice

I run:

MMARGE.pl allele_specific_reads -files S1_shifted_from_CAST_EIJ.sam -ind CAST_EIJ

shown:

Read in mutations for chromosome10 - allele 1 for chromosome11 - allele 1 for chromosome12 - allele 1 for chromosome13 - allele 1 for chromosome14 - allele 1 for chromosome15 - allele 1 for chromosome16 - allele 1 for chromosome17 - allele 1 for chromosome18 - allele 1 for chromosome19 - allele 1 for chromosome1 - allele 1 for chromosome2 - allele 1 for chromosome3 - allele 1 for chromosome4 - allele 1 for chromosome5 - allele 1 for chromosome6 - allele 1 for chromosome7 - allele 1 for chromosome8 - allele 1 for chromosome9 - allele 1 for chromosomeX - allele 1 Processing sam file S1_shifted_from_CAST_EIJ.sam

the -ind files were generated by myself with mm39 as reference.

vlink commented 2 months ago

Hi,

Sorry for the late response. Can you send me your input file so I can test it?

vlink commented 2 weeks ago

Just a general note. The default mapping method for this script is bowtie, so if you used STAR, you need to specify this with -method star. That might explain why you did not get any outputs from your command.

njwehi commented 2 weeks ago

Hi Thanks so much for your response and so sorry that I forgot to prepare the input files. here I attached the sam file and the mutation files. Because of the size limitation, I only included data of chr16

Thanks very much!

CAST_mut.tar.gz d the mutation files. test.sam.gz