Hi group
I am trying to map RNAseq single straneded paired end reads using tophat, the alignment rate I get using samtools falgstat is very good (~90%) however checking the logs files of tophat, specifically, bowties.left.keep.reads shows a very low overall alignment rate (~36%). Can someone please help me understand these parameters ?
Thanks a lot
Alyaa
This is the tophat command I use:
This is the samtools flagstast command:
The logs files; bowtie.left_kept_reads.log
I am trying to map RNAseq single straneded paired end reads using tophat, the alignment rate I get using samtools falgstat is very good (~90%) however checking the logs files of tophat, specifically, bowties.left.keep.reads shows a very low overall alignment rate (~36%). Can someone please help me understand these parameters ?
Thanks a lot
Alyaa
This is the tophat command I use:
Code:
$ tophat -g 1 -p 8 -G test.gtf -o test_thout --library-type fr-firststrand test R1_001.fastq R2_001.fastq
Code:
$ samtools flagstat accepted_hits.bam 36919320 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 36919320 + 0 mapped (100.00%:-nan%) 36919320 + 0 paired in sequencing 18510302 + 0 read1 18409018 + 0 read2 33270470 + 0 properly paired (90.12%:-nan%) 35338762 + 0 with itself and mate mapped 1580558 + 0 singletons (4.28%:-nan%) 406722 + 0 with mate mapped to a different chr 87168 + 0 with mate mapped to a different chr (mapQ>=5)
Code:
19786770 reads; of these: 19786770 (100.00%) were unpaired; of these: 12585633 (63.61%) aligned 0 times 6908036 (34.91%) aligned exactly 1 time 293101 (1.48%) aligned >1 times 36.39% overall alignment rate
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