Hello,
I have two separate left and right mate sam files from a sample's RNAseq data (these are unmapped sam files after running alignment both right and left mate fastq files) and I need to find out which of these reads come from pairs and which of these reads are left unmapped from either just left or right mate. ie. In the end I should be able to calculate this
1- % Reads common in left and right mate sam files
2- %Reads only in left mate sam file
3- %Reads only in right mate sam file
can someone please suggest on how to do it? Should I read the read names in hash and compare the ids?
Thanks!
•
written
by
PAn •
2 answers
You should really map the reads paired, which will (typically) only generate a single sam file containing both mapped and unmapped reads. It's not clear to me how you ended up where you are, or what you're trying to do, but mapping is much more accurate when reads are paired.
I think samtools flagstat will give you that
Log in to answer this question.
-
Get all unmapped read and mate in bam
written by vinaykusuma •
-
how to split forward and reverse reads from sam file
written by Bioinfo •
-
Filtering BAM file to include PE reads that did not map, even though their mate did
written by nute11a •
-
Number of unmapped reads after filtering issue
written by max_19
-
Running pe-utils to find insert length for miso failing
written by spacer •
-
How to extract unmapped Paired end reads from BWA output sam file
written by Bioinfonext
-
Identification of the sequence insertion site in the genome
written by valerie
-
Calculating inner mate distance for paired reads
written by dgimode •
-
How to Separate a SAM File Containing Forward and Reverse Reads into Two Separate Files
written by kdevakan •
-
How To Differentiate Between Mate Pair And Paired End Reads Based On Sam Flag
written by Abhi
