No reads in Output of MMARGE.pl allele_specific_reads - repost

[njwehi]

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]

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]

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