Hello,
I ran an analysis on paired end reads through tophat2 using:
tophat2 -p12 -o <tophat_dir> --no-coverage-search <reference genome> R1.fq R2.fq
and the results gave 1.2% coverage.
I ran the same data through bowtie2
bowtie2 -x <index> -1 <R1.fq> -2 <R2.fq> -S <output.sam> and got a 42.75% overall alignment rate.
Why such a big discrepancy? I tried --coverage-search as well and got the same results.
I checked the tophat run.log and it's putting this into bowtie:
bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 12 --sam-no-hd -x
Any idea what's going on?
P.S. I've been getting a silent error in my tophat.log
bam2fastx: /usr/lib64/libz.so.1: no version information available
and
fix_map_ordering: /usr/lib64/libz.so.1: no version information available
I do have libz.so.1.2.3
The process still runs fine and the bam file output can be used for differential analysis... I just have terrible coverage. Any ideas?
I ran an analysis on paired end reads through tophat2 using:
tophat2 -p12 -o <tophat_dir> --no-coverage-search <reference genome> R1.fq R2.fq
and the results gave 1.2% coverage.
I ran the same data through bowtie2
bowtie2 -x <index> -1 <R1.fq> -2 <R2.fq> -S <output.sam> and got a 42.75% overall alignment rate.
Why such a big discrepancy? I tried --coverage-search as well and got the same results.
I checked the tophat run.log and it's putting this into bowtie:
bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 12 --sam-no-hd -x
Any idea what's going on?
P.S. I've been getting a silent error in my tophat.log
bam2fastx: /usr/lib64/libz.so.1: no version information available
and
fix_map_ordering: /usr/lib64/libz.so.1: no version information available
I do have libz.so.1.2.3
The process still runs fine and the bam file output can be used for differential analysis... I just have terrible coverage. Any ideas?
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