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Hello all,
I've been working with mouse data mostly, and when using Tophat for alignment I've had the following settings:
tophat -p 8 -G $DATA/hg19.mrna.gtf --prefilter-multihits -o $WDIR/tophat_$TAG --segment-length 20 --max-multihits 15 $BOWTIE/hg19 $FQFILE
When working with human samples, I've noticed that more reads remain unaligned on average. This could be due to larger genetic diversity in humans vs. lab mice, if I understand this correctly.
When you guys work with human samples, what settings do you use for alignment? Most of my data is 50bp single-end RNA-seq.
Do you change --segment-mismatches and --read-mismatches?
Thanks in advance
I've been working with mouse data mostly, and when using Tophat for alignment I've had the following settings:
tophat -p 8 -G $DATA/hg19.mrna.gtf --prefilter-multihits -o $WDIR/tophat_$TAG --segment-length 20 --max-multihits 15 $BOWTIE/hg19 $FQFILE
When working with human samples, I've noticed that more reads remain unaligned on average. This could be due to larger genetic diversity in humans vs. lab mice, if I understand this correctly.
When you guys work with human samples, what settings do you use for alignment? Most of my data is 50bp single-end RNA-seq.
Do you change --segment-mismatches and --read-mismatches?
Thanks in advance
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