Hi,
I am unable to run Tophat2 as I get an error.
Here is the command I run: tophat2 -p 5 -r 62 –library-type fr-firststrand -G /home/jmotwani/mydata/Genomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/gene.gtf –o /home/jmotwani/RNASeq/Alignment_Tophat2 --BOWTIE2_INDEXES /home/jmotwani/mydata/Genomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/ C95VLANXX-2046D-01-01-01_L003_R1_Trimmed.fastq C95VLANXX-2046D-01-01-01_L003_R2_Trimmed.fastq
I get the following error:
[2016-05-22 22:20:05] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2016-05-22 22:20:05] Checking for Bowtie
Bowtie version: 2.2.9.0
[2016-05-22 22:20:05] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–library-type.*.bt2l)
The indexed genome was downloaded from Illumina iGenomes page. Do I have to build it after downloading it? I downloaded the genome, gtf file, and indexed files and gave the path of those files in the command above.
Could anyone please comment or advise on this.
Thanks for your time.
Regards, J
I am unable to run Tophat2 as I get an error.
Here is the command I run: tophat2 -p 5 -r 62 –library-type fr-firststrand -G /home/jmotwani/mydata/Genomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/gene.gtf –o /home/jmotwani/RNASeq/Alignment_Tophat2 --BOWTIE2_INDEXES /home/jmotwani/mydata/Genomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/ C95VLANXX-2046D-01-01-01_L003_R1_Trimmed.fastq C95VLANXX-2046D-01-01-01_L003_R2_Trimmed.fastq
I get the following error:
[2016-05-22 22:20:05] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2016-05-22 22:20:05] Checking for Bowtie
Bowtie version: 2.2.9.0
[2016-05-22 22:20:05] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–library-type.*.bt2l)
The indexed genome was downloaded from Illumina iGenomes page. Do I have to build it after downloading it? I downloaded the genome, gtf file, and indexed files and gave the path of those files in the command above.
Could anyone please comment or advise on this.
Thanks for your time.
Regards, J
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