Number of aligned reads in exon, intron ...

Question

[samuelrivero]

Hello,

I am new in RNA-seq. I would like to know how calculate the number (%) of aligned reads in exons, introns in a bam file.

Thanks

[PoGibas]

Welcome to Biostars!

Please check previous questions: Extracting Read Count For Each Gene/Exon From Rna-Seq Bam Files

Answer 1

[mikhail.shugay]

Hi! I'm usually doing this with Picard suite, see http://picard.sourceforge.net/picard-metric-definitions.shtml

Answer 2

[Ido Tamir]

You could try http://rseqc.sourceforge.net/#read-distribution-py also have a look at the other programs from this suite.

Answer 3

[samuelrivero]

Thank you so much for the help. I will check those suites. Do you think using samtools in this way will work?

samtools view -b -F exons.bed aligned.bam > aligned.exons.bam

Thank you again.

Sam

[mikhail.shugay]

You don't need to explicitly use samtools for CollectRNASeqMetrics from Picard (http://picard.sourceforge.net/command-line-overview.shtml#CollectRnaSeqMetrics)

the command line should be following (after downloading and unpacking Picard tools):

java -Xmx4G -jar picard/CollectRnaSeqMetrics.jar REF_FLAT=exome.refFlat INPUT=aligned.bam CHART_OUTPUT=rnaSeqCoverage.pdf OUTPUT=rnaSeqMetrics.txt

the exome.refFlat file for H. Sapiens could be downloaded from here.

for other species check http://hgdownload.cse.ucsc.edu/downloads.html

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