Thread: Tophat/Bowtie
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Old 01-12-2016, 03:32 PM   #1
TPH
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Location: USA

Join Date: Jan 2016
Posts: 19
Question Tophat/Bowtie

Hi, I am self learning tuxedo suite for RNA-seq analysis. I keep getting error messages and some how I can not go forward beyond tophat. I downloaded .gtf file using UCSC browser. Here is the command i used.

tophat --num-threads 8 \
--solexa-quals --max-multihits 10 \
--coverage-search --microexon-search \
--mate-inner-dist 150 \
-o tophat-tumor-out \
--keep-tmp \
-G /path_to_folder_having_.gtf_file/hg19.gtf \
/bowtie-2-2.1.0/indexes/hg19 \
/path_to_folder_having_fastq_files/SRR057634_1.fastq \
/path_to_folder_having_fastq_files/SRR057634_2.fastq

But I get this error message again and again.
/path_to_folder_having_fastq_files/SRR057634_1.fastq: Permission denied

Could anyone can think of any thing why this happens?

Thank you very much.

TPH
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