Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
using bwa to map illumina paired end reads mikeworth Bioinformatics 6 08-13-2013 06:02 PM
What is the minimal number of reads for a small RNA sequence?? Tini Illumina/Solexa 0 12-20-2011 01:44 PM
How to map NCBI SOLiD reads with BWA Chandana Bioinformatics 3 12-04-2010 05:57 AM
small seq reads in GEO? how to map them? vebaev Bioinformatics 0 11-12-2010 10:35 AM
the number of aligned reads by maq and bwa totalnew Bioinformatics 3 12-14-2009 11:18 AM

Thread Tools
Old 07-20-2012, 07:19 AM   #1
Senior Member
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default Is it possible to map small number of reads with bwa?

I created two fastqs with nine reads each. Then I ran them thru bwa sampe but only one end is aligned. I looked at the error message. It seems to me the problem might be due to bwa's inability to estimate insert size in this case. Is it possible for us to tell bwa the insert size? I tried -a 1000 but it didn't work....

[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: too few good pairs
[bwa_sai2sam_pe_core] time elapses: 2.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.31 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec
[bwa_sai2sam_pe_core] print alignments... 0.03 sec
[bwa_sai2sam_pe_core] 9 sequences have been processed.
[main] Version: 0.6.1-r104
[main] CMD: bwa sampe -r @RG\tID:exomeID\tLB:exomeLB\tSM:exomeSM\tPL:illumina\tPU:exomePU -a 2000 ../exome/human_g1k_v37.fasta 1.sai 2.sai dqa_1.fq dqa_2.fq
[main] Real time: 2.583 sec; CPU: 2.348 sec
[samopen] SAM header is present: 84 sequences.
ymc is offline   Reply With Quote

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 01:11 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO