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Old 06-09-2013, 03:04 PM   #41
Baoqing
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sorry, just start to pick up the python, any reminder message freak me out.

Just set up the path right for htseq-count

then run it with my bam files:
samtools view accepted_hits.bam | htseq-count - gene.gtf > counts.txt

While the program was running, there was a warning "claimed to have an aligned mate which could be found. (Is the sam file properly sorted?)

Does this warning "complaining that my file is not pair mated, or do i have to add other arguments for this line to run?

Thanks a lot for your help!

Best,

Last edited by Baoqing; 06-09-2013 at 03:56 PM.
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Old 06-10-2013, 01:35 AM   #42
rboettcher
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Your bam/sam file needs to be name sorted for HTSeq-count, see "samtools sort -n".

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Old 06-10-2013, 07:26 AM   #43
Baoqing
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Thank you, I did sort my bam files though. I have the program to finished running, and it turned out a dataset was produced, does that mean everything is good? Should I just ignore the warning message?

Best,
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Old 06-10-2013, 08:59 AM   #44
dpryan
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Quote:
Originally Posted by Baoqing View Post
Thank you, I did sort my bam files though. I have the program to finished running, and it turned out a dataset was produced, does that mean everything is good? Should I just ignore the warning message?

Best,
See this thread, that's likely what's going on.
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Old 06-10-2013, 12:29 PM   #45
Baoqing
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awesome. The name sorted bam file worked perfect! Really appreciate it!
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Old 01-19-2014, 03:06 PM   #46
gwilymh
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Quote:
Originally Posted by quinlana View Post
If I understand your question correctly, BEDTools has a utility called coverageBed that will compute the raw counts of reads in a BAM file among features in a BED or GTF file.

For example:
Code:
$ coverageBed -abam alignedReads.bam -b transcripts.gtf > transcript.cov.txt
There is also a histogram (-hist) mode that will give you a histogram of coverage for each feature in the -b file. I have not yet updated the manual , but the help (-h) for this tools describes the output format.
Just to clarify, is the depth of coverage of each feature synonymous with the raw counts of reads?
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Old 02-27-2015, 05:51 AM   #47
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How can I get a read count per exon per transcript in a particular gene from BAM file? I tried using htseq-count with id_attr=transcipt_id but this approach does not give me the read count per exon per transcript. I tried using DEXSeq to get the read count, but it does not get what I want. Is there any way to get the read count? I only got one gene of interest to analyse which TPM1. This gene has more than 40 isoforms, so it is possible to get each of the isoforms their read count for each exon. Thanks!
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