Tophat2 RNA seq mapping
1
Hi, I am trying to run tophat2 using following tophat command:
tophat -p 8 -G /scratch/sbag/Tikshana/Ath/index/Bowtie_Ath/Bowtie_Ath -o /scratch/sbag/Tikshana/Ath/map/Athctrl_tophat/ genome /scratch/sbag/Tikshana/Ath/Athctrl_1P.fastq /scratch/sbag/Tikshana/Ath/Athctrl_2P.fastq
I am getting the following error:
Error: cannot find transcript file /scratch/sbag/Tikshana/Ath/index/Bowtie_Ath/Bowtie_Ath*
But the file contains files for indexed reference.
please help me to troubleshoot the problem
RNA-Seq
• 1.8k views
I think this is simply wrong syntax.
Usage: tophat [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]
So -G
must be a GTF file not a folder. Also why is there a whitespace in Athctrl_tophat/ genome
.
It probably must be
tophat -p 8 -G AnyGTFfile.gtf -o /scratch/sbag/Tikshana/Ath/map/Athctrl_tophat/genome /scratch/sbag/Tikshana/Ath/index/Bowtie_Ath/ /scratch/sbag/Tikshana/Ath/Athctrl_1P.fastq /scratch/sbag/Tikshana/Ath/Athctrl_2P.fastq
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If you want to do RNA reads mapping to your reference genome, please use hisat2 tool.
may I know difference between Tophat2 and Hisat2
But the file contains files for indexed reference.
What does that mean? Please show the content of the folder where the index files are in usingls
.Can you post the output of
These are the index output files: Bowtie_Ath.1.bt2 Bowtie_Ath.2.bt2 Bowtie_Ath.3.bt2 Bowtie_Ath.4.bt2 Bowtie_Ath.rev.1.bt2 Bowtie_Ath.rev.2.bt2
That is fine but in which folder are they?
in the above mentioned folder : /scratch/sbag/Tikshana/Ath/index/Bowtie_Ath/