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No reads in Output of MMARGE.pl allele_specific_reads - repost #10

Open njwehi opened 1 month ago

njwehi commented 1 month 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.

here I attached the sam file and the mutation files. Because of the size limitation, I only included data of chr16

CAST_mut.tar.gz test.sam.gz

vlink commented 1 month ago

To me it looks like you mapped the data with STAR. the default for allele_specific_reads is bowtie. Can you re-run it -method star: MMARGE.pl allele_specific_reads -files S1_shifted_from_CAST_EIJ.sam -ind CAST_EIJ -method star

That should fix this.

njwehi commented 1 month ago

Thanks! I will rerun it. I am wondering why the difference between aligner cause such issue?