Hi,
I want to align the Rna-seq data using bowtie2.so here are the steps i did(i installed tophat,bowtie2 and samtools and kept in bashprofile)
i got the reference genome from bowtie2(hg19) and i ran the makescript for indexing them.i got
6 index files(hg19.1.bt2 hg19.2.bt2 hg19.3.bt2 hg19.4.bt2 hg19.rev.1.bt2 hg19.rev.2.bt2)and i kept in genome folder hg19
now i want to run the tophat by takine these index files and the fastq file like this but i am getting error
[ab RNASEQ]$ tophat /net/gs/vol3/shared/lab/RNASEQ/hg19/hg19 C_RNAseq_1.fq
[Thu Nov 29 23:45:21 2012] Beginning TopHat run (v1.4.1)
-----------------------------------------------
[Thu Nov 29 23:45:21 2012] Preparing output location ./tophat_out/
[Thu Nov 29 23:45:21 2012] Checking for Bowtie index files
Error: Could not find Bowtie index files /net/gs/vol3/shared/lab/RNASEQ/hg19.*
can anyone help me with this?i am new in using the tophat
Thank you
I want to align the Rna-seq data using bowtie2.so here are the steps i did(i installed tophat,bowtie2 and samtools and kept in bashprofile)
i got the reference genome from bowtie2(hg19) and i ran the makescript for indexing them.i got
6 index files(hg19.1.bt2 hg19.2.bt2 hg19.3.bt2 hg19.4.bt2 hg19.rev.1.bt2 hg19.rev.2.bt2)and i kept in genome folder hg19
now i want to run the tophat by takine these index files and the fastq file like this but i am getting error
[ab RNASEQ]$ tophat /net/gs/vol3/shared/lab/RNASEQ/hg19/hg19 C_RNAseq_1.fq
[Thu Nov 29 23:45:21 2012] Beginning TopHat run (v1.4.1)
-----------------------------------------------
[Thu Nov 29 23:45:21 2012] Preparing output location ./tophat_out/
[Thu Nov 29 23:45:21 2012] Checking for Bowtie index files
Error: Could not find Bowtie index files /net/gs/vol3/shared/lab/RNASEQ/hg19.*
can anyone help me with this?i am new in using the tophat
Thank you
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