Question: Tophat: bowtie indexing error
0
gravatar for ChillarAnand
3.5 years ago by
ChillarAnand40
India
ChillarAnand40 wrote:

Error Message

Couldn't build bowtie index with err = 1

Previous discussions suggests these
- use both refenrece genome and gtf from the same source
- issue can be with terminology “chr#1” in fasta and “1” in gtf

We have tried previously suggested options, but none seems to be useful in  the context.

P.S: We are analysing Anophele stephensi (not so general species of anopheles) and vectorbase being the source.

Thank you for all suggestions and comments !!

 

Update:

Version:  bowtie==2..2.6

Command:  tophat2 -p 7 -T -G ../../anapholes_stephensi/reference/stephnsi.gtf -o tophat_gtf_out/ ../../anapholes_stephensi/reference/stephensi 1_cutadapt.fastq 2_cutadapt.fastq

Fasta file:  ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000300775.2_ASM30077v2/GCA_000300775.2_ASM30077v2_genomic.fna.gz

bowtie rna-seq tophat • 1.4k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by ChillarAnand40

Can you post the following?

  1. The version of bowtie (or bowtie2)
  2. The exact command you're using
  3. The URL to the fasta file(s)

bowtie/bowtie2 don't use GTF files and also aren't the best choice for RNAseq since they can't handle splicing. Are you instead using tophat2 (yes, this uses bowtie internally)? If so, which version?

ADD REPLYlink written 3.5 years ago by Devon Ryan90k

Added details in question. Thanks.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by ChillarAnand40

Can you post the full log output?

e.g. like here

ADD REPLYlink written 3.5 years ago by genomax67k
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