Question: How many should multiple alignment of tophat-out in Human RNA-seqs?
gravatar for Leila Kian
11 months ago by
Leila Kian10
Leila Kian10 wrote:


I'm checking my tophat output data and I would like to know the rate of this multiple alignments are acceptable or not

whether is dependent this rate of multiple alignments to type of genome or not? this RNA-seqs have belonged to Human.

Reads: Input : 36238973 Mapped : 30511468 (84.2% of input) of these: 14351857 (47.0%) have multiple alignments (15253 have >20) 84.2% overall read mapping rate.

thanks in advance

rna-seq tophat alignment • 664 views
ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 11 months ago by Leila Kian10
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The multiple alignment rate seems high. But, this could be how you set up the job parameters with Tophat/Tophat2 (I'm not sure which are you using, and that may not matter going forward). Tophat/Tophat2 have been deprecated. Please use HISAT2 instead.

To retain more or fewer alignments per query sequence (primary alignments, secondary alignments), the parameters can be tuned. For HISAT2, please see:

More help:

  • Galaxy NGS QA/QC plus RNA-seq Tutorials:

  • Search prior Q&A at where there is much discussion about mapping tools, reported alignments, fastq QA (trimming, adaptor removal), and how different parameters can impact mapping rates/reported alignments.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k
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