Question: 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?
0
gravatar for nsknadendla
2.7 years ago by
France
nsknadendla0 wrote:

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. 

bow tie small dna reads • 1.0k views
ADD COMMENTlink modified 2.7 years ago by Israel Barrantes670 • written 2.7 years ago by nsknadendla0
1
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum101k wrote:

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

ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum101k
0
gravatar for Israel Barrantes
2.7 years ago by
Germany
Israel Barrantes670 wrote:

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

ADD COMMENTlink written 2.7 years ago by Israel Barrantes670
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