|Thread||Thread Starter||Forum||Replies||Last Post|
|Enable pairing in a bam file separately aligned by lanes||ty23991||Bioinformatics||5||02-11-2016 03:07 PM|
|Extract reference and aligned sequences from BAM file basing on VCF file||floem7||Bioinformatics||3||01-19-2015 03:08 AM|
|Extract aligned reads from a BAM file above a certain threshold||The Snow||Bioinformatics||4||07-29-2013 02:02 AM|
|FastQ to aligned BAM file Question - Galaxy||Zapages||Bioinformatics||4||05-27-2013 10:09 AM|
|Extract aligned sequence coordinates from SAM or BAM file||pirates.genome||Bioinformatics||5||08-20-2012 08:06 AM|
|03-18-2017, 04:32 PM||#1|
Join Date: Mar 2017
Does BAM file from SRA contain aligned reads?
Hello, everyone. I need to do SNP calling for the first time, so I have a couple questions.
For example, I want to use this sample https://trace.ncbi.nlm.nih.gov/Trace...run=SRR1295568
I can download from there reads in FASTQ format, align them on the reference genome using BWA, for example. After that I will get SAM file, then BAM file and so on.
But also, I can download BAM file from SRA(you choose this option on the bottom line).
As I understand, this file already contains aligned on the reference genome reads. So you don't need to align them, this work is already done, just launch SAMTools, bcftools and do SNPcalling.
So, my questions:
1) Am I right?
2) If Yes, is it better to align reads by yourself, using BWA, or just download BAM file? Would be there some differences in result?
|03-19-2017, 01:02 AM||#2|
David Eccles (gringer)
Location: Wellington, New Zealand
Join Date: May 2011
I generally prefer doing my own read cleaning and alignment, because then I know precisely the process that was used for read filtering and mapping. From my own memory of how submissions work, I think the BAM files in SRA are aligned using whatever method the experimenter decided to use.
|03-22-2017, 04:43 AM||#3|
Location: Research Triangle Park, NC
Join Date: Aug 2009
As mentioned, the BAM files you download were prepared and uploaded by the submitter (FASTQ, while supported, is not a preferred format for SRA and is accepted as reference sequences for the aligned read files). So, if you read their methods and are happy with their QC cutoffs and mapping approach, you could use their BAM files. If not, you need to get the actual read files and do your own reference mapping.
Also take note of how old any submission is and what reference release they used. You may want to re-align the reads to a more recent reference build anyway.
A lot of times, yes, it would make little if any difference how you proceed. Sometimes though, it might. Look through the information provided about the submission and decide for yourself how you wish to proceed.
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
|bam, snpcalling, sra|