Hi, I'm very new at RNASeq Analysis and I think that I'm doing something wrong.
I've tried to align that data: http://trace.ncbi.nlm.nih.gov/Traces...mple=SRS167019.
First I execute sratoolkit to extract the fastq files with this command:
Then I have two files: 1_SRR097897_1.fastq and 1_SRR097897_2.fastq.
The next step that I've done is to execute TopHat to generate the bam file with the reads aligned. The command was:
Then I use the IGB to visualize the results and than shows the + and the - strands are the same 

If I only use one of the _n files to generate the output I have two strands with polarity, but depending on the file to select the polarity is reversed.

I have also tried running TopHat with different parameters enabling --library-type or a GFF annotation file with identical results.
I could stay only with the results obtained through _2.fastq file but I wonder to know what I'm doing wrong, for other occasions.
Thanks for your time!!
I've tried to align that data: http://trace.ncbi.nlm.nih.gov/Traces...mple=SRS167019.
First I execute sratoolkit to extract the fastq files with this command:
fastq-dump --split-3 ./1_SRR097897.sra
The next step that I've done is to execute TopHat to generate the bam file with the reads aligned. The command was:
../tophat2 -N 0 Pombe 1_SRR097897_1.fastq 1_SRR097897_2.fastq


If I only use one of the _n files to generate the output I have two strands with polarity, but depending on the file to select the polarity is reversed.

I have also tried running TopHat with different parameters enabling --library-type or a GFF annotation file with identical results.
I could stay only with the results obtained through _2.fastq file but I wonder to know what I'm doing wrong, for other occasions.
Thanks for your time!!
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