Question: STAR aligner concordant read
0
gravatar for krushnach80
2.1 years ago by
krushnach80630
krushnach80630 wrote:

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 • 828 views
ADD COMMENTlink modified 2.1 years ago by michael.ante3.5k • written 2.1 years ago by krushnach80630
2
gravatar for michael.ante
2.1 years ago by
michael.ante3.5k
Austria/Vienna
michael.ante3.5k wrote:

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

ADD COMMENTlink written 2.1 years ago by michael.ante3.5k

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

ADD REPLYlink written 2.1 years ago by krushnach80630

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.

ADD REPLYlink written 2.1 years ago by michael.ante3.5k
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