Re: [Bio-bwa-help] Soft clipping using bwa aln

[VG <gup...@gm...>]

Hi Joseph,
Thank you for the response. The reason I want the soft clipping is because
the reads are chimeric. So I first want to align the reads with miRBASE
with seed length =24 and allowing for 3 mismatches in 24 bp(mature miRNA
length). And the the soft clipped part of the read with genome so as to see
where is the second part of the read coming from. That is the reason I want
to have soft clipping sequences. I have already taken care of adapter
contamination. Do you think this can be done in bwa? My reads are single end

Regards
Varun

On Thu, Apr 2, 2015 at 2:05 PM, Joseph Fass <jos...@gm...> wrote:

> Hi Varun,
>
> bwa *sampe* will produce clipped alignments when a read doesn't
> originally align (at whatever settings are used in bwa aln), but the read's
> partner aligns. sampe (if I'm not mistaken) then performs a more sensitive
> search near that aligned partner read. Since it's only a small search area,
> this doesn't cost a lot, computationally.
>
> So, bwa *samse* can't take advantage of partner reads, since you're not
> aligning paired end reads, so it only finds *global* alignments of each
> read (local within the reference genome, global with respect to the read).
>
> What's the reason you think you need to see soft clipping? If your reads
> have adapter sequence, or low quality stretches, then trimming first might
> be better. Or, if you think there's enough variation between the reference
> genome and what you sequenced, you could use bwa mem.
>
> Hope that helps,
> ~Joe
>
> On Wed, Apr 1, 2015 at 1:28 PM, VG <gup...@gm...> wrote:
>
>> HI,
>> I am using bwa 0.7.9a and I am using bwa aln to align raw fastq reads to
>> my custom genome which consists of unique miRNA sequences. I built the
>> index using this command
>>
>> /apps1/bwa/0.7.9a/gnu/bin/bwa index -p INDEX mature_miRNA_seq.fa
>>
>> Then I used bwa aln for mapping
>>
>> /apps1/bwa/0.7.9a/gnu/bin/bwa aln -n 3 -k 3 -t 4 -l 24 /user/INDEX
>> test.fastq > test.sai
>>
>> and then used
>>
>> /apps1/bwa/0.7.9a/gnu/bin/bwa samse -f test.sam /user/INDEX test.sai
>> test.fastq
>>
>> I can see my sam is produced but no reads with soft clipping. Does bwa
>> aln does soft clipping?
>>
>> I want to have soft clipping sequences in my CIGAR STRING. What can I do??
>>
>> Regards
>> Varun
>>
>>
>>
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>
>
> --
> Joseph Fass
> Lead Data Analyst
> UC Davis Genome Center - Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> jn...@uc...
> phone ~ 530.752.2698
>