Hi,
I'm working on RNA-seq data (Illumina Hi-Seq). After Trimmomatic, CLC (de novo assembly) and MIRA assembly and adding the Debris, I run Tophat to map my raw reads against the transcriptome.
Here's the code and the alignment summary:
tophat -p 64 -o Path/to/Output /path/to/bowtie/database /path/to/Paired_forward.fq.gz /path/to/Paired_reverse.fq.gz
The Output I get is:
This already does look not too good for me.
After sorting with samtools (samtools -n), express gives me about 10-30 hits per sample.
Does anybody have any idea what might be going wrong here?
Thanks a lot!
I'm working on RNA-seq data (Illumina Hi-Seq). After Trimmomatic, CLC (de novo assembly) and MIRA assembly and adding the Debris, I run Tophat to map my raw reads against the transcriptome.
Here's the code and the alignment summary:
tophat -p 64 -o Path/to/Output /path/to/bowtie/database /path/to/Paired_forward.fq.gz /path/to/Paired_reverse.fq.gz
The Output I get is:
Left reads
Input: 11157893
Mapped: 10404612 (93.2% of Input)
of These: 8239736 (79.2%) have multiple alignments (1167061 have >20)
Right reads
Input: 11157893
Mapped: 10404612 (93.2% of Input)
of These: 8239736 (79.2%) have multiple alignments (1167061 have >20)
93.2% Overall read mapping rate.
Aligned pairs: 10404612
of These: 8239769 (79.2%) have multiple alignments
10404497 (100.0%) are discordant alignments
0.0% concordant pair alignment rate.
Input: 11157893
Mapped: 10404612 (93.2% of Input)
of These: 8239736 (79.2%) have multiple alignments (1167061 have >20)
Right reads
Input: 11157893
Mapped: 10404612 (93.2% of Input)
of These: 8239736 (79.2%) have multiple alignments (1167061 have >20)
93.2% Overall read mapping rate.
Aligned pairs: 10404612
of These: 8239769 (79.2%) have multiple alignments
10404497 (100.0%) are discordant alignments
0.0% concordant pair alignment rate.
After sorting with samtools (samtools -n), express gives me about 10-30 hits per sample.
Does anybody have any idea what might be going wrong here?
Thanks a lot!
Comment