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Old 08-07-2015, 02:27 PM   #1
idedios
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Default bwa mis-alignment of TruSeq Amplicon reads



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.
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Old 08-07-2015, 03:34 PM   #2
Bukowski
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Cross posted to Biostars: https://www.biostars.org/p/153442/
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Old 08-10-2015, 03:48 PM   #3
idedios
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Any comments?
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Old 08-11-2015, 11:22 AM   #4
idedios
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So based on a reply from biostars it looks like the BaseSpace reads have been trimmed. Now I just need to understand how they trimmed it. This is desirable since my alignment has led to the variant caller calling a lot of false indels.

It's possible that Illumina is trimming the reads based on the regions in their manifest file. If I could do the same then maybe I could get the reads I'm looking for.
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Old 08-11-2015, 11:32 AM   #5
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You are likely doing an apples to oranges comparison (especially since you don't know the complete details of how BaseSpace analysis is being done). BaseSpace is also likely using isaac/isaac2 for the alignments (or do you know that they are using bwa).

What is it that you are trying to do? Replicate BaseSpace analysis locally (with same software/parameters)?
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Old 08-11-2015, 11:55 AM   #6
Brian Bushnell
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Is it even the same data? The reads appear to be different lengths.
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Old 08-11-2015, 12:32 PM   #7
idedios
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The reads are from the same fastqs. I'm just trying to figure out why my alignment is looking so messy when the TruSeq Amplicon stuff is supposed to have strictly sized blocks of reads. It is possible they are using the isaac aligner so I'll have to do more tinkering to figure out what is going on.
I'm doing this to move my BaseSpace analyses in-house using bcbio-nextgen.
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Old 08-11-2015, 01:48 PM   #8
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Quote:
Originally Posted by idedios View Post
I'm doing this to move my BaseSpace analyses in-house using bcbio-nextgen.
Is this what you are planning to use: https://github.com/chapmanb/bcbio-nextgen? Does not seem to include a trimming program at first glance (which you should plan to include).
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Old 08-11-2015, 02:19 PM   #9
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Quote:
Originally Posted by GenoMax View Post
Is this what you are planning to use: https://github.com/chapmanb/bcbio-nextgen? Does not seem to include a trimming program at first glance (which you should plan to include).
Yeah this is exactly what I am using. I could ask Brad Chapman about a trimming program.
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