search

alexdobin / STAR

RNA-seq aligner
MIT License
1.77k stars 495 forks source link

Output SAM file contains only QNAMEs from forward fasta not reversed #2113

Open mirachirkova opened 2 months ago

mirachirkova commented 2 months ago

Hello! I use STAR to create SAM file from two fasta files. I have tried many combinations of options, however every time output file doesn’t contain QNAMEs from reversed fasta. It seems that this QNAMEs were replaced by paired names from forward fasta.

All names from forward fasta ends with “a” and all names from reversed fasta ends with “b”. That’s example of output I get: Screenshot from 2024-04-10 14-13-50

But in the same project, where I get input fasta’s, there is an example of STAR output and it looks like that: Screenshot from 2024-04-10 14-16-57

Could you, please, help me to understand, why do I get results without “b”’s?

My command line:

STAR --runThreadN 64 --genomeDir ${directory with index} --readFilesIn ${forward fasta} ${reverse fasta} --twopassMode Basic --outSAMunmapped Within --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000 --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3 --seedSearchStartLmax 50 --alignSJoverhangMin 5 --alignEndsType Local --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66 --winAnchorMultimapNmax 50 --alignSJDBoverhangMin 3 --outFilterType Normal

I've tried STAR versions 2.7.10a and 2.5.0a and results are the same.

Best wishes, Miroslava

alexdobin commented 2 months ago

Hi Miroslava,

STAR only uses the read name provided in the first file in the --readFilesIn option. Naming the reads differently is against SAM format rules. If you need to do it, you would have to write a script that will rename after mapping.