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Thread | Thread Starter | Forum | Replies | Last Post |
BWA alignment followed by TopHat | slny | Bioinformatics | 9 | 06-06-2011 07:19 AM |
How does Tophat rank alignment? | hyj004 | Bioinformatics | 0 | 01-19-2011 02:54 PM |
tophat total alignment | zorph | Bioinformatics | 4 | 12-09-2010 05:09 AM |
Understanding tophat intermediate logs | laxman | RNA Sequencing | 2 | 10-23-2010 06:25 PM |
TopHat alignment issue | telos | Bioinformatics | 0 | 03-16-2010 11:39 AM |
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#1 |
Junior Member
Location: NYC Join Date: Mar 2012
Posts: 2
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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 |
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#2 |
Junior Member
Location: us Join Date: Aug 2015
Posts: 2
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Hi,liueagle,
I just run into the same problem, have you figure it out? Thanks! Best, Ellie |
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