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