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Old 06-30-2015, 03:38 AM   #1
Postdoc Cancer Bioinformatics
Location: Olso, Norway

Join Date: Dec 2014
Posts: 17
Default transcriptome_index Bowtie2 Index

Dear all,

As far as understand Tophat2 creates an transcriptome_index which also includes Bowtie2 Index files using GTF and the genome file. Then why do we need to supply Bowtie2 Index to create transcriptome index for the first time.

I tried to create transcriptome index without supplying bowtie2 index files and it gave following error.

tophat2 -G ../data/Homo_sapiens.GRCh37.75.gtf --transcriptome-index ./transcriptome_index/ ../data/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa

[2015-06-30 12:25:22] Building transcriptome files with TopHat v2.0.13
[2015-06-30 12:25:22] Checking for Bowtie
Bowtie version:
[2015-06-30 12:25:24] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (../data/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.*.bt2)

However, after that I created bowtie2 index files and ran same process and no error was produced.
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