Convert Settings From Bowtie To Bowtie2

Question

[lsvijfhuizen]

Dear All,

I want to change from Bowtie to Bowtie2 since Bowtie2 supportes gapped alignments. Normally I used to following command in Bowtie:

bowtie -k 1 -m 1 -n 1 -p 1 -S --best --strata reference.fa file.fastq file.sam 2>>results.summary

-k 1 = report up to 1 valid alignments
-m 1 = instructs bowtie to refrain from reporting any alignments for reads having more than 1 reportable alignments.
-n 1 = Maximum number of mismatches
-p 1 = Launch parallel search threads 
-S =  File to write SAM alignments
--best--strata = Specifying --strata in addition to --best causes bowtie to report only those alignments in the best alignment "stratum".

I want to use the same settings in Bowtie2 and add the function to allow for one gap with maximal 2 bp in that specific gap. Can anyone help me with changing the settings?

Thank you!

[Zev.Kronenberg]

Please take the time to read the Bowtie2 manual.

Answer 1

[Istvan Albert]

First of all there is no automatic conversion that would save you time. At least I have not heard of any such approach.

As Zev.Kronenberg points out please look at the Bowtie2 manual and you will find answers for most of your questions. Come back with issues that may still linger.

[lsvijfhuizen]

Hi Istvan, you and Zev are right. I thought maybe there is an approach to change every code automatically. But if there isn't something for it, I will have a look at the Bowtie2 Manual. Thanks for your replay!