Question: How many read files i can use in tophat in the same run?
0
gravatar for A
4.2 years ago by
A3.6k
A3.6k wrote:

good morning friends,

supposing i have and experiment with 10 samples and each with just sra file...in 

tophat -r 20 test_ref reads_1.fq reads_2.fq  syntax i should mention all of my fastq files??? if yes, may you please tell me the order of files..i mean for example i should type reads_1.fq -> reads_10.fq  ???

thanks a lot

myposts rna-seq tophat • 1.1k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by A3.6k
1

Run tophat on each sample separately (or write a simple bash script with a list of fastq file names as input and specify different output directory for each of them). In case of paired-end  reads_1.fq and reads_2.fq defines for Right and Left.

ADD REPLYlink written 4.2 years ago by Anushka20
4
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Each sample must be aligned independently. You can not give tophat all of the files for all of the samples at one time and get multiple output files.

ADD COMMENTlink written 4.2 years ago by Devon Ryan92k

thanks Devon,

sorry

i placed the orf_coding.fasta (my reference genome) in the bowtie2 file and indexed the genome in the same bowtie2, and run this syntax but error,

may you please tell me a solution?

[izadi@lbox161 bowtie2-2.2.5]$ $TOP/tophat -r 20 orf_coding.fasta SRR1944914_trimmed.fastq SRR1944926_trimmed.fastq

[2015-09-01 10:27:50] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-01 10:27:50] Checking for Bowtie
          Bowtie version:     2.2.5.0
[2015-09-01 10:27:50] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (orf_coding.fasta.*.bt2)
[izadi@lbox161 bowtie2-2.2.5]$ $TOP/tophat -r 20 orf_coding.fasta SRR1944914_trimmed_unmapped.fastq SRR1944926_trimmed_unmapped.fastq

[2015-09-01 10:29:01] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-01 10:29:01] Checking for Bowtie
          Bowtie version:     2.2.5.0
[2015-09-01 10:29:01] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (orf_coding.fasta.*.bt2)
[izadi@lbox161 bowtie2-2.2.5]$ 

ADD REPLYlink written 4.2 years ago by A3.6k
2

This part of the error message should tell you what to fix: Error: Could not find Bowtie 2 index files (orf_coding.fasta.*.bt2)

 

ADD REPLYlink written 4.2 years ago by Devon Ryan92k

sorry,

but after indexing there are coding.1.bt2, coding.2.bt2, coding.3.bt2, coding.4.bt2, coding.rev.1.bt2 and coding.rev.2.bt2

and orf_coding.fasta in bowtie2 file...then what i should provide?

ADD REPLYlink written 4.2 years ago by A3.6k
2

Then you need to write coding rather than orf_coding.fasta.

ADD REPLYlink written 4.2 years ago by Devon Ryan92k

thanksssssssssssssssssssssss a lot Devon, you saved me i was getting mad since yesterday...

ADD REPLYlink written 4.2 years ago by A3.6k
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