How to Pick out reads from certain locus

[HSV-1]

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!

[dariober]

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:

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

[HSV-1]

Hi- Either load your BAM file in a genome viewer like IGV and find locus TP53 and/or extract the relevant reads wth samtools:

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 ?

[paolo.kunder]

it should be the 10th column:

cut -f10 mylocus.sam > myfastq.fq