[Guest]

Hi everybody!

I starting using bowtie today, i wanted to align csfasta + qual file width the bowtie.
I build the reference fasta file width the bowtie-build, after that i try to align the csfasta+qual file to the reference file(s), but i have error massege.
The bowtie-build command:

bowtie-build -C reference_genom.fa ref/reference_genom

The bowtie command:

bowtie -C ref/reference_genom -f read.csfasta -Q quality.qual -S align.sam

And the error command with my bowtie commnad:

bowtie -C ref/reference_genom -f read.csfasta -Q quality.qual -S align.sam
/usr/include/seqan/sequence/string_base.h:237 Assertion failed : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) was: 48 >= 48 (Trying to access an element behind the last one!)
Aborted

The csfasta file contains only short reads, every sequances are 50 bp long.

My question is that what is the error mean? I try to search this error message but don't found anything.
I installed the bowtie width the following way:

sudo apt-get install bowtie

I really appreciate any help/answer.
Thank you!

[TiborNagy]

This means something is wrong with you csfasta or quality file.

[fereshteh]

Hi Ben,
really happy that i can talk with you here because at first when i was working with bowtie2 i asked myself how much you can be clever that created bowtie and how much i am not who cant run bowtie properly...
anyway i have a question about --un option:
if i want to separate mapped and unmapped reads when aligning, which code i should type???
bowtie2 -x [name of the bowtie2-build indicized file containing the rRNA sequence] --un [name of the fastq file which will contain the UNMAPPED reads] -U [name of the fastq file containing the reads] -S [name of the .sam file that will contain the MAPPED and UNMAPPED reads]
I could not understand about --un option because i don't know which i should type instead of [name of the fastq file which will contain the UNMAPPED reads]

[dpryan]

I'm obviously not Ben, but "--un unmapped.fastq" or "--un sample.unmapped.fastq" or something along those lines would be common. Pick a name that makes sense to you, it doesn't matter what it is.

[Arpitha]

Nice work Ben. Happy to that im here!

[seqan]

Hi all,

Sorry to resurrect this topic, but my workflow depends on Bowtie (not Bowtie2) so I'd like to ask for an advice on the following issue:

In a couple of published paired-end datasets, I encountered a problem that long reads are being mapped OK, but reads shorter than 100 bp in one dataset (or shorter than 150 bp in another dataset) don't get mapped. I am using Bowtie with the following parameters:

-t -v 2 -m 1 --solexa-quals hg19 -1 [reads file 1] -2 [reads file 2]

Could you please suggest what's going wrong?

Thanks!