SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA alignment followed by TopHat slny Bioinformatics 9 06-06-2011 06:19 AM
How does Tophat rank alignment? hyj004 Bioinformatics 0 01-19-2011 01:54 PM
tophat total alignment zorph Bioinformatics 4 12-09-2010 04:09 AM
Understanding tophat intermediate logs laxman RNA Sequencing 2 10-23-2010 05:25 PM
TopHat alignment issue telos Bioinformatics 0 03-16-2010 10:39 AM

Reply
 
Thread Tools
Old 07-13-2012, 11:22 AM   #1
liueagle
Junior Member
 
Location: NYC

Join Date: Mar 2012
Posts: 2
Default TopHat alignment logs

Dear all,

Here is something I am confusing when I see the log file produced by TopHat:
This is the TopHat.log:
.
[2012-06-06 18:09:24] Preparing reads
left reads: min. length=36, max. length=101, 91637851 kept reads (29218 discarded)
[2012-06-06 19:03:03] Creating transcriptome data files..
[2012-06-06 19:03:48] Building Bowtie index from genes.fa
[2012-06-06 19:33:23] Mapping left_kept_reads to transcriptome genes with Bowtie2
[2012-06-06 23:43:22] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-06-07 00:41:00] Resuming TopHat pipeline with unmapped reads
[2012-06-07 00:47:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2
[2012-06-07 05:40:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2012-06-07 07:18:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2012-06-07 09:29:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2012-06-07 11:18:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)


And I also look at the 6 bowtie log files:
bowtie.left_kept_reads.fixmap.log
bowtie.left_kept_reads.m2g_um.fixmap.log
bowtie.left_kept_reads.m2g_um_seg1.fixmap.log
bowtie.left_kept_reads.m2g_um_seg2.fixmap.log
bowtie.left_kept_reads.m2g_um_seg3.fixmap.log
bowtie.left_kept_reads.m2g_um_seg4.fixmap.log

There are the details:

more logs/bowtie.left_kept_reads.fixmap.log
91637851 reads; of these:
91637851 (100.00%) were unpaired; of these:
18520354 (20.21%) aligned 0 times
23392329 (25.53%) aligned exactly 1 time
49725168 (54.26%) aligned >1 times
79.79% overall alignment rate

more logs/bowtie.left_kept_reads.m2g_um.fixmap.log
31718744 reads; of these:
31718744 (100.00%) were unpaired; of these:
4069491 (12.83%) aligned 0 times
22890602 (72.17%) aligned exactly 1 time
4758651 (15.00%) aligned >1 times
87.17% overall alignment rate

more logs/bowtie.left_kept_reads.m2g_um_seg1.fixmap.log
12545530 reads; of these:
12545530 (100.00%) were unpaired; of these:
10313519 (82.21%) aligned 0 times
1421598 (11.33%) aligned exactly 1 time
810413 (6.46%) aligned >1 times
17.79% overall alignment rate

more logs/bowtie.left_kept_reads.m2g_um_seg2.fixmap.log
12496456 reads; of these:
12496456 (100.00%) were unpaired; of these:
10103227 (80.85%) aligned 0 times
1477840 (11.83%) aligned exactly 1 time
915389 (7.33%) aligned >1 times
19.15% overall alignment rate

more logs/bowtie.left_kept_reads.m2g_um_seg3.fixmap.log
12092205 reads; of these:
12092205 (100.00%) were unpaired; of these:
10185446 (84.23%) aligned 0 times
1143907 (9.46%) aligned exactly 1 time
762852 (6.31%) aligned >1 times
15.77% overall alignment rate

more logs/bowtie.left_kept_reads.m2g_um_seg4.fixmap.log
9205319 reads; of these:
9205319 (100.00%) were unpaired; of these:
8181576 (88.88%) aligned 0 times
581085 (6.31%) aligned exactly 1 time
442658 (4.81%) aligned >1 times
11.12% overall alignment rate


Now I am confusing the relationship with these numbers: 18520354, 31718744, 12545530, 12496456, 12092205 and 9205319. I did not see that the reads aligned 0 times in left_kept_reads equal the total reads of all the m2g_um alignment reads?
Could you tell me how tophat do the alignment in detail: such as firstly aligning the exon; then aligning the unmapping reads to junction regions? But the number of reads mapping reads to junction regions do not equal to the reads of
liueagle is offline   Reply With Quote
Old 09-29-2015, 03:32 PM   #2
ellieduan
Junior Member
 
Location: us

Join Date: Aug 2015
Posts: 2
Default

Hi,liueagle,
I just run into the same problem, have you figure it out?
Thanks!

Best,
Ellie
ellieduan is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:06 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO