BWA interpretation and Resources

Question

[zggayk]

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

Answer 1

[Sean Davis]

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.

[zggayk]

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

[GouthamAtla]

samtools flagstat works on bam file.