Hi, everyone!
I'm worried about my mapping results with TopHat2.
I'm working with five sets of reads and these are the mapping results:
S1 - 65.8 %
S2 - 29.6 %
S3 - 80.3 %
S4 - 15.4 %
S5 - 65.3 %
I am mapping them to a reference genome with a gtf file with a command like this:
$ tophat -p 8 -G genes.gtf -o C1_R1_thout --library-type=fr-unstranded \
genome C1_R1_1.fq C1_R1_2.fq
What should I do about the S2 and S4?
Would it be worth to try to map all samples with other tool like trinity or should I take a look to unmapped reads in BLAT or the best thing to would be to loose my parameters with a higher value of "--read-mismatches", "--read-gap-length", "--read-edit-dist"?
Thanks a lot since now and best regards?
I'm worried about my mapping results with TopHat2.
I'm working with five sets of reads and these are the mapping results:
S1 - 65.8 %
S2 - 29.6 %
S3 - 80.3 %
S4 - 15.4 %
S5 - 65.3 %
I am mapping them to a reference genome with a gtf file with a command like this:
$ tophat -p 8 -G genes.gtf -o C1_R1_thout --library-type=fr-unstranded \
genome C1_R1_1.fq C1_R1_2.fq
What should I do about the S2 and S4?
Would it be worth to try to map all samples with other tool like trinity or should I take a look to unmapped reads in BLAT or the best thing to would be to loose my parameters with a higher value of "--read-mismatches", "--read-gap-length", "--read-edit-dist"?
Thanks a lot since now and best regards?
Comment