Bowtie2 limit local alignment to 5' end

gwl186 · 11-15-2012, 01:46 PM

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

KatrinSameith · 02-18-2014, 01:50 AM

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

vishnuamaram · 02-18-2014, 01:52 AM

Hey KatrinSameith,

Try using FASTXTOOLKIT, with this you can specifically trim.

gwl186 · 02-18-2014, 04:59 AM

Quote:

Originally Posted by KatrinSameith

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

KatrinSameith · 02-18-2014, 05:05 AM

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

Joelvet · 01-29-2019, 11:27 PM

plz try Prinseq-lite and Tag cleaner to trim ends of your reads

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11-15-2012, 01:46 PM	#1
gwl186 Junior Member Location: China Join Date: May 2012 Posts: 2	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

02-18-2014, 01:50 AM	#2
KatrinSameith Member Location: Dresden, Germany Join Date: Jan 2014 Posts: 10	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

02-18-2014, 01:52 AM	#3
vishnuamaram Member Location: india Join Date: Jun 2013 Posts: 42	Hey KatrinSameith, Try using FASTXTOOLKIT, with this you can specifically trim.

02-18-2014, 05:05 AM	#5
KatrinSameith Member Location: Dresden, Germany Join Date: Jan 2014 Posts: 10	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

01-29-2019, 11:27 PM	#6
Joelvet Junior Member Location: India Join Date: Nov 2018 Posts: 2	plz try Prinseq-lite and Tag cleaner to trim ends of your reads