TopHat alignment logs

[liueagle]

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

[ellieduan]

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

Best,
Ellie