I have a problem. I try aligning paired end data of restrictive heart cardiomyopathy using tophat and I get this summary:
tophat2 -o trialtophatRestrictive3 -p 20 -G /data2/hg19/genes.gtf /data2/hg19/genome SRR2138385_1.fastq SRR2138385_2.fastq
Left reads:
Input : 56776839
Mapped : 54092930 (95.3% of input)
of these: 3069097 ( 5.7%) have multiple alignments (4267 have >20)
Right reads:
Input : 56776839
Mapped : 420422 ( 0.7% of input)
of these: 21837 ( 5.2%) have multiple alignments (32 have >20)
48.0% overall read mapping rate.
Aligned pairs: 411231
of these: 21368 ( 5.2%) have multiple alignments
8215 ( 2.0%) are discordant alignments
The left reads map 95% while the right reads map only 0.7%
What should I do?
I did fastqc before tophat and the reports for the forward and reverse were fine.
I appreciate your help
Thanks alot
Sarah
tophat2 -o trialtophatRestrictive3 -p 20 -G /data2/hg19/genes.gtf /data2/hg19/genome SRR2138385_1.fastq SRR2138385_2.fastq
Left reads:
Input : 56776839
Mapped : 54092930 (95.3% of input)
of these: 3069097 ( 5.7%) have multiple alignments (4267 have >20)
Right reads:
Input : 56776839
Mapped : 420422 ( 0.7% of input)
of these: 21837 ( 5.2%) have multiple alignments (32 have >20)
48.0% overall read mapping rate.
Aligned pairs: 411231
of these: 21368 ( 5.2%) have multiple alignments
8215 ( 2.0%) are discordant alignments
The left reads map 95% while the right reads map only 0.7%
What should I do?
I did fastqc before tophat and the reports for the forward and reverse were fine.
I appreciate your help
Thanks alot
Sarah
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