miRNA mapping using BOWTIE - Page 2

dukevn · 08-16-2010, 03:32 PM

Anybody knows how I can trim out the adapter sequence with a certain number of mismatch (1 or 2)?

Thanks,

D.

didymos · 08-17-2010, 01:32 AM

Hi,

In Bowtie you can trim n nucleotides from 3' or 5' end with -3 n or -5 n option - so you can play with this and -v 2 for two mm. However for trimming I am using blast with smaller word size -W option, and then choosing only those mappings which are on the 3' end.

tomek

dukevn · 08-17-2010, 11:52 AM

Quote:

Originally Posted by didymos

Hi,

In Bowtie you can trim n nucleotides from 3' or 5' end with -3 n or -5 n option - so you can play with this and -v 2 for two mm. However for trimming I am using blast with smaller word size -W option, and then choosing only those mappings which are on the 3' end.

tomek

Thanks, but I want to trim the adapter sequence, not n nucleotides.

mgogol · 11-03-2010, 02:35 PM

fastx_clipper can trim adapter sequence.

jdanderson · 11-03-2010, 04:59 PM

Hello Everyone,

I would like to second mgogol's suggestion. It is part of a larger set of tools called FASTX Toolkit: http://hannonlab.cshl.edu/fastx_toolkit/index.html

I've found the tools to be very useful and user friendly.

Cheers,
Johnathon

zeam · 06-27-2011, 11:07 PM

Hi everyone,
When you were processing smRNA-seq data,which software did you use?I have attempted SOAP2 and bowtie,both of them didn't work well enough,many of the reads could not map to the reference.But when I used blat,it works well except consuming time.Can you guys give me some suggestions?My data is from plants,and I want to sepate miRNA and siRNA from smRNA-seq data.
Thanks!

NicoBxl · 06-28-2011, 12:16 AM

did you allow mismatches in your alignment ?

zeam · 06-28-2011, 01:47 AM

Quote:

Originally Posted by NicoBxl

did you allow mismatches in your alignment ?

What I want is to dissect the correlation between smRNA and DNA methylation.Previous studies reveals that both of miRNA and siRNA involed in DNA methylation.The problem I met is 1)mapping;2)separating miRNA and siRNA from smRNA-seq data.Can you give me some suggestions if you have some experience on these subjects?

unique379 · 05-09-2013, 06:42 AM

Dear all,

as above discussions and suggestion, could i use bowtie something like this for miRNA alignment ?? just please make me sure.

bowtie --sam -q -n 0 -l 15 -e 99999 -k 200 -a --chunkmbs 1024 --best ....

JonB · 06-10-2013, 06:25 AM

Quote:

Originally Posted by yjhua2110

in our deepBase database, we use options: –k 200 –v 0. the Specifying the parameters (–k 200 –v 0) instructs Bowtie to report up to 200 perfect hits for each read.

deepBase is a platform for annotating and discovering small and long ncRNAs from next generation sequencing data. It is available at http://deepbase.sysu.edu.cn

I am mapping reads from a small RNA sequencing, and I am curious how you treat the results after mapping with the -k 200 option? Do you assemble the transcripts? Or do you report all the locations where a read has been mapped?

sBeier · 06-10-2013, 07:05 AM

Usually, with small RNAs being not bigger than 24 nt, you would filter for reads between maybe 15 - 28 nt length. Those are the complete transcripts, so no need for any assembly.

JonB · 06-10-2013, 10:44 AM

Could you run a program like Cufflinks specifying a mean transcript length of about 18 nts, and then get a gtf file of the different transcripts?

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08-16-2010, 03:32 PM	#21
dukevn Member Location: RI Join Date: Apr 2009 Posts: 50	Anybody knows how I can trim out the adapter sequence with a certain number of mismatch (1 or 2)? Thanks, D.

08-17-2010, 01:32 AM	#22
didymos Junior Member Location: Poland Join Date: Jun 2010 Posts: 8	Hi, In Bowtie you can trim n nucleotides from 3' or 5' end with -3 n or -5 n option - so you can play with this and -v 2 for two mm. However for trimming I am using blast with smaller word size -W option, and then choosing only those mappings which are on the 3' end. tomek

11-03-2010, 02:35 PM	#24
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	fastx_clipper can trim adapter sequence.

11-03-2010, 04:59 PM	#25
jdanderson Member Location: Davis, CA Join Date: Sep 2010 Posts: 45	Hello Everyone, I would like to second mgogol's suggestion. It is part of a larger set of tools called FASTX Toolkit: http://hannonlab.cshl.edu/fastx_toolkit/index.html I've found the tools to be very useful and user friendly. Cheers, Johnathon

06-27-2011, 11:07 PM	#26
zeam Member Location: USA Join Date: Oct 2010 Posts: 38	Hi everyone, When you were processing smRNA-seq data,which software did you use?I have attempted SOAP2 and bowtie,both of them didn't work well enough,many of the reads could not map to the reference.But when I used blat,it works well except consuming time.Can you guys give me some suggestions?My data is from plants,and I want to sepate miRNA and siRNA from smRNA-seq data. Thanks!

06-28-2011, 12:16 AM	#27
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	did you allow mismatches in your alignment ?

05-09-2013, 06:42 AM	#29
unique379 Member Location: Italy Join Date: Aug 2012 Posts: 27	Dear all, as above discussions and suggestion, could i use bowtie something like this for miRNA alignment ?? just please make me sure. bowtie --sam -q -n 0 -l 15 -e 99999 -k 200 -a --chunkmbs 1024 --best ....

06-10-2013, 07:05 AM	#31
sBeier Member Location: Germany Join Date: Jan 2013 Posts: 42	Usually, with small RNAs being not bigger than 24 nt, you would filter for reads between maybe 15 - 28 nt length. Those are the complete transcripts, so no need for any assembly.

06-10-2013, 10:44 AM	#32
JonB Member Location: Norway Join Date: Jan 2010 Posts: 83	Could you run a program like Cufflinks specifying a mean transcript length of about 18 nts, and then get a gtf file of the different transcripts?