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Old 11-15-2012, 12:46 PM   #1
gwl186
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Question Bowtie2 limit local alignment to 5' end

Hi all,

I'm using bowtie2 to do the local alignment. However, we are thinking the 5' end will have enough good sequencing quality, while 3' end may not. We are trying to use local alignment option to map the reads. However, I found the result will allow soft trimming on both 5' and 3' end. Could I only limit it to only allow trimming on 3' end but not 5' end? I didn't find any option in bowtie2.

Do anyone have suggestions for me to do this?

Best, Weilong
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Old 02-18-2014, 12:50 AM   #2
KatrinSameith
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Hi Weilong,

did you find a way around your problem? I am facing a similar question, so I push your post up again. Is it possible for --local alignments to just trim the 3' end?

Would be happy for any advise! Thanks in advance.
Katrin
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Old 02-18-2014, 12:52 AM   #3
vishnuamaram
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Hey KatrinSameith,

Try using FASTXTOOLKIT, with this you can specifically trim.
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Old 02-18-2014, 03:59 AM   #4
gwl186
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Quote:
Originally Posted by KatrinSameith View Post
Hi Weilong,

did you find a way around your problem? I am facing a similar question, so I push your post up again. Is it possible for --local alignments to just trim the 3' end?

Would be happy for any advise! Thanks in advance.
Katrin
Hi KatrinSameith,

Not yet. I haven't find any way to get around the problem only using bowtie2. Maybe other tools could be used to get around this. Such as Vishnuamaram's suggestion.

Weilong
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Old 02-18-2014, 04:05 AM   #5
KatrinSameith
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Dear vishnuamaram and Weilong,

Thank you for your replies. I will try fastx_clipper or cutadapt to trim one-sided first (I am dealing with adaptor sequences) and then run --end-to-end alignments.

--local alignments was my first idea, because I thought I would circumvent the trimming step. But never mind, it makes sense and it seems to be required.

Thanks again & have a nice day,
Katrin
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Old 01-29-2019, 10:27 PM   #6
Joelvet
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plz try Prinseq-lite and Tag cleaner to trim ends of your reads
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