Tophat sequence aligner does not work properly
I am trying to use tophat to align my fastq reads to the reference genome.
I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.
Then I am running the following command to run tophat.
I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).

The tophat output directory(sample_thout) has been created but it contains only the following files.

Inside the log I can see the following:

Inside tmp I can see these files:
I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?
alignment rna-seq
asked Nov 22 '18 at 22:51
yas.f
8419
add a comment |
I am trying to use tophat to align my fastq reads to the reference genome.
I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.
Then I am running the following command to run tophat.
I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).

The tophat output directory(sample_thout) has been created but it contains only the following files.

Inside the log I can see the following:

Inside tmp I can see these files:

I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?
alignment rna-seq
asked Nov 22 '18 at 22:51
yas.f
8419
add a comment |
I am trying to use tophat to align my fastq reads to the reference genome.
I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.
Then I am running the following command to run tophat.
I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).

The tophat output directory(sample_thout) has been created but it contains only the following files.

Inside the log I can see the following:

Inside tmp I can see these files:

I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?
alignment rna-seq
asked Nov 22 '18 at 22:51
yas.f
8419
I am trying to use tophat to align my fastq reads to the reference genome.
I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.
Then I am running the following command to run tophat.
I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).

The tophat output directory(sample_thout) has been created but it contains only the following files.

Inside the log I can see the following:

Inside tmp I can see these files:

I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?
alignment rna-seq
alignment rna-seq
asked Nov 22 '18 at 22:51
yas.f
8419
asked Nov 22 '18 at 22:51
yas.f
8419
asked Nov 22 '18 at 22:51
yas.f
8419
asked Nov 22 '18 at 22:51
yas.f
8419
asked Nov 22 '18 at 22:51
yas.f
8419
8419
add a comment |
add a comment |
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