SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Problem with alignment: I can only align 10% of reads(CLIP data, tophat/bowtie) 610617109 Bioinformatics 13 11-09-2015 07:09 AM
Bowtie alignment Bakhtiyar Taghizada Bioinformatics 1 03-11-2014 09:07 AM
bowtie index problem (bowtie-build and then bowtie-inspect) tgenahmet Bioinformatics 4 09-10-2013 11:51 AM
Bowtie alignment for ChIP-seq: good alignment for input but not for ChIP sample nico_z Bioinformatics 2 03-20-2013 10:19 AM
alignment with bowtie maria_mari Bioinformatics 1 02-01-2012 12:19 PM

Reply
 
Thread Tools
Old 07-15-2016, 04:12 AM   #1
Linas
Junior Member
 
Location: Lithuania

Join Date: Jul 2016
Posts: 3
Default Problem with Bowtie alignment

Novice here. I tried to align miRNA sequencing data (Illumina) with mature miRNA from mirbase.org database using Bowtie. Reads are adapter trimmed and mapped to human genome hg19 by someone else. Length is about 26 nt. However, i get very small portion of aligned reads to mature miRNAs (less than 1%). I have tried options: -n 0 -l 20 (-l 17 - no difference). However, even those reads that got aligned were weird because of the length of the aligned reads in an output.

I then experimented with some mirna sequences to see how do results look in a more controlled manner: i aligned sequence from reference genome (mature miRNAs) with a indexed mature miRNAs reference. Of course, it got aligned but in a output it wrote some 13 nucleotide sequence that was not in input.
Input was 22 nt:
>hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p
UGAGGUAGUAGGUUGUAUAGUU.

Output was 13 nt:
hsa-let-7a-5p MIMAT0000062 Homo sapiens let-7a-5p + hsa-let-7a-5p 0 GAGGAGAGGGAAG IIIIIIIIIIIII 0

I would like to know what this output means. As far as i know the sequence should be the sequence that got aligned. If i trimm (-3 <int> or -5 <int) the 13 nt sequence shortens by a indicated number.
Linas is offline   Reply With Quote
Old 07-17-2016, 12:11 AM   #2
Linas
Junior Member
 
Location: Lithuania

Join Date: Jul 2016
Posts: 3
Default

It appears that bowtie do not print out U nucleotides. However, could it be the problem of low mapping percentage that input is sequence data (that is cDNA) and reference is mature miRNA?
Linas is offline   Reply With Quote
Reply

Tags
alignment, bowtie, output

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:40 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO