Error Regarding Bowtie2 Run

Question

[Raghav]

hello every one, I have got an error during the running bowtie2 command my command is

 [cdac@nbri bowtie2-2.1.0]$ bowtie2 -x Arab_Ref -1 /storage/home/cdac/raghav/sratoolkit.2.3.2-4-centos_linux64/bin/SRR681003_1.fastq -2 /storage/home/cdac/raghav/sratoolkit.2.3.2-4-centos_linux64/bin/SRR681003_2.fastq -S SRR_wild.sam

I have got an msg bowtie2-align exited with value 1. I don't know how to remove it. Any one may help me out.

your valuable comments and suggestions are always welcome.

[Istvan Albert]

you really need to provide more information on the error, exiting with value 1 is not sufficient information to troubleshoot

[tianhan313]

Dear Raghav, after I installed Bowtie2, I tried to run it, I meet the same problem as you, "bowtie2-align exited with value 1". Could you tell me how to solve this problem? Thank You!

Answer 1

[Raghav]

Dear Istvan Albert, Sir the problem has been resolved now.

I would like to ask one thing, how do we write syntax which help me to search chimeric reads??? . how to customize bowtie2 syntax for capturing chimeric reads??

Any read become chimeric if it aligned at tow different locations of reference genome. say for example, read1 is 100nts long and and is a chimeric read if and only if when it's starting 30 nts mapped on chromosome1 at 100 to 130 position and remaining parts of read mapped on chromosome1(may another chromosome) at 10000 to 10060 positions,

I want to costumize botwie2 according to my requirement which I have mentioned above. please suggest me if you could help me.

[Istvan Albert]

Please do not add a new question as the answer! Read the message in blue below on the proper way to communicate on this site. In general you should always ask a new question independently.