Tophat Alignment Summary.txt

[arcolombo698]

Hello.

I am running a single stranded alignment on Tophat v.2.0.10
and according to the manual, we have to library options, first strand and second strand.

I completed my alignments for the first strand and have somewhat of a low mapping rate.
According to the manual , the only way to check which library to use is to run the first and second strands and compare results.

I am now running the library type -secondstrand and awaiting the results.

I am just seeking general advice on how to process this correctly. thank you


Left reads:
Input : 35732348
Mapped : 16332729 (45.7% of input)
of these: 476549 ( 2.9%) have multiple alignments (4626 have >20)
Right reads:
Input : 35732348
Mapped : 16383018 (45.8% of input)
of these: 426962 ( 2.6%) have multiple alignments (4550 have >20)
45.8% overall read mapping rate.

Aligned pairs: 14952780
of these: 374540 ( 2.5%) have multiple alignments
80381 ( 0.5%) are discordant alignments
41.6% concordant pair alignment rate.

[arcolombo698]

Junctions.bed

More importantly, the manual says that I need to count the junctions in the file junctions.bed


how do I understand the output from the junctions.bed file.

ie.

where are the junctions in


track name=junctions description="TopHat junctions"
chr1 11628 12100 JUNC00000001 2 + 11628 12100 255,0,0 2 43,91 0,381
chr1 14698 15038 JUNC00000002 56 - 14698 15038 255,0,0 2 131,69 0,271
chr1 14969 15859 JUNC00000003 10 - 14969 15859 255,0,0 2 69,64 0,826
chr1 15922 16720 JUNC00000004 2 - 15922 16720 255,0,0 2 25,114 0,684
chr1 16646 16988 JUNC00000005 180 - 16646 16988 255,0,0 2 119,131 0,211
chr1 16923 17363 JUNC00000006 353 - 16923 17363 255,0,0 2 132,131 0,309
chr1 16953 17706 JUNC00000007 4 - 16953 17706 255,0,0 2 102,101 0,652
chr1 16945 17969 JUNC00000008 7 - 16945 17969 255,0,0 2 110,55 0,969
chr1 17238 17737 JUNC00000009 53 - 17238 17737 255,0,0 2 130,132 0,367
chr1 17612 18023 JUNC00000010 164 - 17612 18023 255,0,0 2 130,109 0,302