Hi everyone,
I'm sorry if it is answered anywhere else, I have raw dna-seq paired-end sequence reads data from different libraries of read length for different samples. Ranging from 50-90, 50-101, 50-150 (after quality trimming). In FASTQC check i noticed that about 10% of reads are lesser than 70 bp for each sample.
As BWA-mem is pretty mature now but the bwa docs say that bwa mem is preferable for longer reads ( > 70 bp). and BWA-aln is good for shorter reads, but i guess most of the reads from my library are not shorter.
I want to use one mapping algorithm for consistency reasons.Can i still use bwa-mem ignoring small fraction of smaller read lengths? or i should use BWA-aln ?
Thanks
sohail
0 answers
No answers yet.
Log in to answer this question.
-
BWA mem minimum read length
written by yolek64754 •
-
BWA_MEM SHORT READS
written by Phismil •
-
Fastq screen: use bwa aln and not bwa mem
written by Matteo •
-
BWA mem and BWA aln lead to different results
written by zhangdezhi008 •
-
BWA aln vs. mem for 100bp reads
written by ropolocan
-
Why ExAC used bwa aln instead of mem?
written by abascalfederico
-
alignment with BWA mem
written by mra8187 •
-
BWA mem vs. Sampe alignment
written by kirannbishwa01
-
BWA mem vs BWA sampe alignment
written by kirannbishwa01
-
When and why is bwa aln better then bwa mem?
written by dariober
bwa-mem could be used for short reads as well, but this blog suggests that
bwa-alnperforms better for 50bp reads but over allmemhas a good accuracy at different mismatch levels. Would it be useful if you align the 10% of the short reads withmemandalnand compare the stats to see if it makes a big difference.yes, i think i should try to compare..