How to send .txt file with short reads of DNA into Bow Tie and obtain an output with the sequences not aligned to a reference genome (hg19)? Please suggest a java api to perform this task?

Question

[nsknadendla]

Hi I have generated some random DNA reads and want to send them to Bow Tie as a .txt file and retrieve output with the DNA codes that cannot be aligned for a given reference genome. I would appreciate if anyone working on it could send me an api in java to send short reads to Bow tie remotely to see the non aligned reads. Thank you in advance.

Answer 1

[Pierre Lindenbaum]

Bowtie reads fastq files. http://en.wikipedia.org/wiki/FASTQ_format

Bowtie produces BAM files: You can filter a BAM file with samtools to extract the unmapped reads.

You can call Bowtie from java http://www.mkyong.com/java/how-to-execute-shell-command-from-java/

remotely ?: you can always code a java server calling bowtie (good luck !) : http://plindenbaum.blogspot.fr/2013/04/java-jni-bindings-for-bwamem-lite.html

Answer 2

[Israel Barrantes]

Bowtie2 outputs unaligned reads from a FASTQ when specifying the --un flag. Details [here]