STAR aligner concordant read

Question

[1769mkc]

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

Answer 1

[michael.ante]

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

[1769mkc]

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

[michael.ante]

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.