Question: Tophat Both Pairs Must Map Concordantly
0
gravatar for AW
5.3 years ago by
AW350
United Kingdom
AW350 wrote:

Hi,

I have run tophat with the following parameters, specifying each reads can only map once and that they must map concordantly.

 tophat2 --solexa1.3-quals -p 12 -r 80 --read-mismatches 0 --max-multihits 1 --no-mixed --no-discordant

Therefore why do I have to following output in the align_summary.txt. Were the reads that mapped multiply discarded? ​

Left reads:
               Input:  23815106
              Mapped:   9138883 (38.4% of input)
            of these:     92429 ( 1.0%) have multiple alignments (77607 have >1)
Right reads:
               Input:  23844741
              Mapped:   9168518 (38.5% of input)
            of these:     92790 ( 1.0%) have multiple alignments (77715 have >1)
38.4% overall read alignment rate.

Aligned pairs:   7091314
     of these:     10745 ( 0.2%) have multiple alignments
          and:    250038 ( 3.5%) are discordant alignments
28.7% concordant pair alignment rate.

Thanks

tophat2 • 1.8k views
ADD COMMENTlink modified 5.3 years ago by Istvan Albert ♦♦ 80k • written 5.3 years ago by AW350
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1071 users visited in the last hour