Hi!
I am proceeding my samples alignment using Tophat2 (below, an example of the command used).
tophat2 -G Homo_sapiens.GRCh37.75.gtf -p 5 -o MSCd0Adip-11 Hsa_GRCh37_75 SRR490216.fastq
When the alignmente is finished, the file "align_summary.txt" shows the report below. I have more than 60,000 reads, but only 601 mapped. Does anybody knows why is this happening?
Why my reads are not mapping? How can I fix this?
Reads:
Input: 69492
Mapped: 601 ( 0.9% of input)
of these: 53 ( 8.8%) have multiple alignments (0 have >20)
0.9% overall read alignment rate.
Thank you!!
I am proceeding my samples alignment using Tophat2 (below, an example of the command used).
tophat2 -G Homo_sapiens.GRCh37.75.gtf -p 5 -o MSCd0Adip-11 Hsa_GRCh37_75 SRR490216.fastq
When the alignmente is finished, the file "align_summary.txt" shows the report below. I have more than 60,000 reads, but only 601 mapped. Does anybody knows why is this happening?
Why my reads are not mapping? How can I fix this?
Reads:
Input: 69492
Mapped: 601 ( 0.9% of input)
of these: 53 ( 8.8%) have multiple alignments (0 have >20)
0.9% overall read alignment rate.
Thank you!!
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