Question: bwa mem to feature Counts
gravatar for ajajoo
7 weeks ago by
ajajoo0 wrote:

bwa mem -t $Ncpu -k 14 -T 1 -L 3,3 -O 6,6 -E 3,3 ../humangenomes/hg38.fa $filename.R1.fastq.gz $filename.R2.fastq.gz | samtools view -Sbh > $filename.bam

Can I use above bam file for feature counts, how will it handle chimeric alignment and what is the quality for linear match with the above parameters. Is there any away I can filter bam file from above command to pass it to feature count. This is what I use right now.

featureCounts -p -T 5 -a hg38GENCODE.gtf -o $filename.txt $filename.bam &

I am running data in bulk, that requires bwa mem with above parameters so do not want to use resources for e.g. STAR alignment etc for passing it to featureCount.

I am very new to this field, so please direct me to good literature for all these things. I am still understanding bwa mem algo and how these parameters will affect the results.

featurecounts bwa mem • 91 views
ADD COMMENTlink modified 7 weeks ago by swbarnes2340 • written 7 weeks ago by ajajoo0
Answer: bwa mem to feature Counts
gravatar for swbarnes2
7 weeks ago by
swbarnes2340 wrote:

I'm pretty sure bwa-mem is not splice aware, so it's not suitable for RNASeq. You really should use STAR.

ADD COMMENTlink written 7 weeks ago by swbarnes2340

Or use Bioconductor software Rsubread::align and Rsubread::featureCounts. This is the Bioconductor forum after all!

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by Gordon Smyth39k
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