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
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tikshyadav19 •
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
nice catch ! alternatively:
tophat -p 8 /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
Ideally one would do a special transcriptome index creation run one-time as described in TopHat2 manual.
tophat -G known_genes.gtf \
--transcriptome-index=transcriptome_data/known \
hg19
Then use the index produced for actual read alignments
tophat -o out_sample1 -p4 \
--transcriptome-index=transcriptome_data/known \
hg19 sample1_1.fq.z sample1_2.fq.z &
tophat -o out_sample2 -p4 \
--transcriptome-index=transcriptome_data/known \
hg19 sample2_1.fq.z sample2_2.fq.z &
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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
If you want to do RNA reads mapping to your reference genome, please use hisat2 tool.
may I know difference between Tophat2 and Hisat2
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/