BWA MEM alignment
2
0
Entering edit mode
4 months ago
Qboy • 0

Happy New Year,

I have a question regarding BWA (this is my first time doing it). I have a nice working script for paired-end reads. However, when I converted my SRA files to Fastq, I used fastq-dump --split-3, because I am also interested in small reads due to the quality of DNA I am working on now.

Questions:

  1. Fastq generated three files fastq, fastq_1, fastq_2. Is it possible to put all three to bwa mem? Or what is the best strategy in this case?
  2. I have some files which are single reads. Can I use BWA MEM for single reads too (quality of DNA is low meaning I have more short reads than long, and the longest is about 100 bp)?
mem bwa alignment • 501 views
ADD COMMENT
1
Entering edit mode
4 months ago

The third file usually contains the index sequences associated with sample multiplexing. There is no need to align those.

You can align both single-end and paired-end reads, just not in the same invocation of the command. Basically you would need to run it separately for each data.

ADD COMMENT
0
Entering edit mode

Thank you so much! I think I am now a bit more confident with my next step! Merci

ADD REPLY
1
Entering edit mode
4 months ago
Raman2 ▴ 30
  1. Use fastq_1 and fastq_2 for bwa-mem. (btw, fastq-dump is an older tool. The newer fasterq-dump is faster, multi-threaded and can download and generate fastq files from SRA from a single command line)
  2. Yes, bwa-mem works for single end data
ADD COMMENT

Login before adding your answer.

Traffic: 1775 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6