Hello I am trying to use the Burrows-Wheeler Aligner to align our de novo assembled contigs to a reference genome. I am trying to use the BWA-sw algorithm for this. I have some suspicion because of the output file (in the form of a .sam file) that the alignment did not work properly. Below is a small portion of the file:
@SQ SN:scaffold356 LN:823
@SQ SN:scaffold476 LN:7212
@SQ SN:scaffold211 LN:3330
@SQ SN:scaffold336 LN:2422
@SQ SN:scaffold406 LN:17574
@SQ SN:Scaffold596 LN:5070
@SQ SN:scaffold151 LN:9921
@SQ SN:scaffold516 LN:15906
@SQ SN:scaffold316 LN:9962
@SQ SN:scaffold321 LN:27663
@SQ SN:scaffold431 LN:16280
@SQ SN:scaffold311 LN:47646
@SQ SN:scaffold601 LN:17621
@SQ SN:scaffold701 LN:13490
@SQ SN:scaffold216 LN:82533
@SQ SN:scaffold726 LN:38736
@SQ SN:scaffold101 LN:35666
@SQ SN:scaffold71 LN:42933
@SQ SN:scaffold186 LN:47996
@SQ SN:scaffold731 LN:37331
@SQ SN:Scaffold921 LN:7475
@SQ SN:scaffold111 LN:31478
@SQ SN:scaffold846 LN:25557
I used the following to get to this point:
bwa index -p RTLOindx -a bwtsw Gavia_stellata.fa
bwa bwasw RTLOindx test-scaffolds.fa > test-scaffolds.sam
Other than this forum, are there any detailed example scripts for BWA available anywhere? I have looked at several documentation pages for BWA and they were less than revealing to this novice. Supposing I get our reference alignment to work eventually, are there any good tools for visualization of BWA produced .sam or .bam files? I have looked at one called tablet, but was not able to get this to work with a different .bam file. Thank you very much for your help.
Sincerely,
Zach Gayk
The first few lines that you posted look like a perfectly valid SAM file, so unless there is another problem, you can proceed to convert to BAM. IGV is a good viewer for BAM files.
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written
by
Sean Davis
Thank you very much. I got our alignment to display in the IGV. I was skeptical if the .sam file was accurate, because I was having trouble using the samtools flagstat command, but apparently the bwa alignment did work.
I am now going to try to merge our alignments of contigs and raw reads when I figure out how to do so.
Thanks for your help,
Zach
samtools flagstat works on bam file.
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written
by
GouthamAtla
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