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Old 09-14-2013, 08:58 PM   #1
HSV-1
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Cool How to Pick out reads from certain locus

Hi, all
I want to see all the reads derived from TP53 in a RNA-seq dataset.
How to do this?

I have searched the forum I didn't find the similar post.


Thanks!
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Old 09-15-2013, 12:50 AM   #2
dariober
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Quote:
Originally Posted by HSV-1 View Post
I want to see all the reads derived from TP53 in a RNA-seq dataset.
Hi- Either load your BAM file in a genome viewer like IGV and find locus TP53 and/or extract the relevant reads wth samtools:

Code:
samtools index my_rnaseq.bam ## Skip if index file is present
samtools view my_rnaseq.bam chr1:1-10000 > mylocus.sam
Where "chr1:1-10000" should be replaced with the coordinates of your locus.

Hope this helps
Dario
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Old 09-15-2013, 08:00 PM   #3
HSV-1
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Location: asia

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Quote:
Originally Posted by dariober View Post
Hi- Either load your BAM file in a genome viewer like IGV and find locus TP53 and/or extract the relevant reads wth samtools:

Code:
samtools index my_rnaseq.bam ## Skip if index file is present
samtools view my_rnaseq.bam chr1:1-10000 > mylocus.sam
Where "chr1:1-10000" should be replaced with the coordinates of your locus.

Hope this helps
Dario
Thanks, Dario.
How can I output a fastq file at this point ?
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Old 09-18-2013, 12:51 AM   #4
paolo.kunder
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it should be the 10th column:

cut -f10 mylocus.sam > myfastq.fq
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