Question: bwa misalignment for TruSeq Amplicon reads
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gravatar for idedios
3.8 years ago by
idedios30
USA/Irvine/NeoGenomics Laboratories
idedios30 wrote:

I'm having the following issues using bwa mem on paired-end TruSeq Amplicon reads. I used the default settings with mem. The top sequence is from bwa mem. The bottom is from Illumina's BaseSpace analysis.

bwa truseq amplicon illumina • 1.8k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by idedios30
0
gravatar for idedios
3.8 years ago by
idedios30
USA/Irvine/NeoGenomics Laboratories
idedios30 wrote:

Any comments?

ADD COMMENTlink written 3.8 years ago by idedios30

You didn't ask a question. This isn't an answer. Biostars isn't a forum, it'a Q&A, so these posts should be answers to questions. You didn't have a question in the original post. 

 

I guess you dont like that the top part of the image has red and blue colored reads? See how the Illumina basespace has shorter reads? They have been trimmed, which will impact alignment. 

ADD REPLYlink written 3.8 years ago by karl.stamm3.5k

Thanks this was the answer I was looking for.

I didn't know why bwa was doing what it was or how Illumina made their reads look the way they did. All I knew was that because of my "un-trimmed" reads vardict was calling a lot of false indels.

ADD REPLYlink written 3.8 years ago by idedios30

So the next question is what did Illumina trim from their reads to make it look the way they did? Usually the only trim settings I come by are trimming the adapters but that's definitely not the case here. I have a .bed file with the regions each amplicon should cover.

Is there a way to trim the reads in the bam file so that only what is covered in the bed reference file is kept?

ADD REPLYlink written 3.8 years ago by idedios30
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