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STAR aligner concordant read

I m using star aligner to align the reads , how to get the concordant and discordant read % like we get in tophat2 as i m moving out from tophat due to the time taken here is my command i m using this command 

STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --runThreadN 30 --genomeDir /run/media/punit/data2/star_index --readFilesIn /run/media/punit/data2/OM_STAR_ALIGNER/RD1_trimmed_1.fastq /run/media/punit/data2/OM_STAR_ALIGNER/RD1_trimmed_2.fastq

Any help or suggestion how do get concordant and discordant in my alignment statistics after aligning with STAR

rna-seq
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updated by michael.ante michael.ante • written by 1769mkc 1769mkc

1 answer

Hi,

you can use Picard-tools' CollectAlignmentSummaryMetrics or RSeQC's bam_stat.py in order to collect information about the proper paired reads.

If you use samtools flagstat, be aware of the fact that this is reporting on alignment rather than on read-level.

Cheers,

Michael

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written by michael.ante michael.ante

As a matter of fact i did install this RSeQC's but i can;t call it , im not sure what is the issue .I did a python install as it was mentioned in the RSeQC's manual but i can;t call the command .Can you tell me the issue

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written by 1769mkc 1769mkc

I'd open a new thread about this problem or ask the RSeQC team. When doing so, please provide more information what you did and where an error message was given.

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written by michael.ante michael.ante

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