To check how well the sequencing parts were done, I used bowtie to map all the reads from RNA-seq directly to human refseqs, and I got only 22% (of ) of reads have at least one hit, 78% failed to align, which I think is impossible.
my command is:
"bowtie -p 5 -m 10 -f trx -1 mate1.fa -2 mate2.fa >output"
The output:
# reads processed: 130653415
# reads with at least one reported alignment: 28765542 (22.02%)
# reads that failed to align: 101882364 (77.98%)
# reads with alignments suppressed due to -m: 5509 (0.00%)
Reported 28765542 paired-end alignments to 1 output stream(s)
Any idea why so few reads got mapped? what did I do wrong?
Thank you very much,
Iris
my command is:
"bowtie -p 5 -m 10 -f trx -1 mate1.fa -2 mate2.fa >output"
The output:
# reads processed: 130653415
# reads with at least one reported alignment: 28765542 (22.02%)
# reads that failed to align: 101882364 (77.98%)
# reads with alignments suppressed due to -m: 5509 (0.00%)
Reported 28765542 paired-end alignments to 1 output stream(s)
Any idea why so few reads got mapped? what did I do wrong?
Thank you very much,
Iris
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