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Old 07-06-2011, 11:51 AM   #1
camelbbs
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Default question about tophat

I am running tophat index/mm9 1.fastq

to get accepted_hist.bam

The running process has no error. But 1.fastq has 1Gb, accepted_hist.bam only has 470K.

So What does it mean? It means only a few reads has mapped to reference genome?

I downloaded mm9 from bowtie website and contructed a .fa file using bowtie-inspect mm9 > mm9.fa

Anyone know this problem?

thanks!
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Old 07-07-2011, 12:23 PM   #2
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I am curious why no people reply this? anyone can help?
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Old 07-07-2011, 12:48 PM   #3
chadn737
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Did you check look at your alignment file to see if anything was aligned or check the tophat log files?
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Old 07-07-2011, 01:32 PM   #4
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thanks, I have checked my result , I really got some result but the result number is so small.
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Old 07-07-2011, 01:49 PM   #5
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Quote:
Originally Posted by chadn737 View Post
Did you check look at your alignment file to see if anything was aligned or check the tophat log files?
Hi chadn737,

May you recommend some good method to extract gene expression from RNA seq data.

Now I am using tophat and cufflinks but the result seems not I want.

BTW, does the reference genome mm9 I used is right?
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Old 07-07-2011, 02:08 PM   #6
shurjo
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Quote:
Originally Posted by camelbbs View Post
I am running tophat index/mm9 1.fastq

to get accepted_hist.bam

The running process has no error. But 1.fastq has 1Gb, accepted_hist.bam only has 470K.

So What does it mean? It means only a few reads has mapped to reference genome?

I downloaded mm9 from bowtie website and contructed a .fa file using bowtie-inspect mm9 > mm9.fa

Anyone know this problem?

thanks!
This is absolutely normal. accepted_hits.bam is in the binary BAM format which uses much less space than fastq (which is in text format).
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Old 07-07-2011, 02:46 PM   #7
chadn737
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Quote:
Originally Posted by shurjo
This is absolutely normal. accepted_hits.bam is in the binary BAM format which uses much less space than fastq (which is in text format).
True, but 470K is a very small bam file, even for a small data set of only 1GB.
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Old 07-07-2011, 07:24 PM   #8
shurjo
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Quote:
Originally Posted by chadn737 View Post
True, but 470K is a very small bam file, even for a small data set of only 1GB.
Agreed. Maybe we will get a better insight after camelbbs looks at the actual BAM file to see what's in it.

Another option would be to run FastQC on the input file to check the quality of the reads.
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