Question: Error: Could not find Bowtie 2 index files (splice-mismatch.*.bt2)
0
gravatar for ALI Hkz
10 weeks ago by
ALI Hkz0
Italy/Siena
ALI Hkz0 wrote:

hi i am running tophat2 and bowtie2 , these are my commands and i couldn't get the result:

tophat2 -p 16 --keep-fasta-order -o ./tophat_out_${NAME}\
 --read-mismatches 4\
 --read-gap-length 4\
 --read-edit-dist 4\
 --read-realign-edit-dist 0\
 --min-anchor 4\
 -- splice-mismatch 1\
 --GTF gencode.v19.annotation.gtf\
 --transcriptome-index= transcriptome/\
 genome/Homo_sapiens.bowtie_index\
 trimmed_cut1SRR5481725.fastq trimmed_cut2SRR5481725.fastq

and that's the error massage that i face:

[2018-12-05 09:23:33] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (splice-mismatch.*.bt2)
ADD COMMENTlink modified 10 weeks ago by Devon Ryan88k • written 10 weeks ago by ALI Hkz0
1

Please do not use Tophat anymore, the author himself said it's outdated

HISAT2 and STAR are both splice aware solution

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Bastien Herv√©3.3k

Hmmm the command you show doesn't match with the error you get?

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k
4
gravatar for Devon Ryan
10 weeks ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

You have a space in -- splice-mismatch. As mentioned in the comment, you should not be using tophat for anything.

ADD COMMENTlink written 10 weeks ago by Devon Ryan88k
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