Hey All, I am trying to do RNA seq on CLC, but before transfer my data to the program I need to split the reads that I have into forwarding and reverse. There is a program called fastq-dump -I --split-files that does this process. The problem which I have is the 75 RNA seq files has it's own SRR number. I tried many times to run the program for all my RNA seq reads but every time it gets failed. Can you please tell me what I should do? Your help is highly appreciated Thanks Mustafa
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mustafa_aljadi •
3 answers
Hi, You can try the first parallel-fastq dump which split the SRA file using all threads so its, faster. First download the parallel-fastq dump and then run the following script, it will run in loop for all sra file and split using ncbi-sra tool kit.
Just define number of threads available and the output directory. Put this script in your sra file directory and change permission with chmod u+x script.
#!/bin/bash
fastq_dump(){
for i in *.sra
do
echo "Starting the dump"
parallel-fastq-dump -s $i --split-3 --threads 16 -O /outputdir --gzip --tmpdir /temp_dir
echo "Completed dump"
done
}
fastq_dump
Just get fastq files directly from EBI-ENA. You can use a neat tool called SRA-explorer to generate URL's for all sequenes you want to download. See: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
You can get fastq files directly from ENA. Outlined in this tutorial: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
It also covers usage of prefetch and (parallel-)fastq-dump if you want to go with that.
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I already download the files from NCBI. To transfer the 75 RNA seq files to CLC program those files need to be split into reverse and forward. I did use this code fastq-dump -I --split-files SRR390728.sra, which is applicable for example for one SRR390728. My question is how can I split the 75 RNA seq files together without using SRR numbers? Thanks Mustafa
@padwalmk has a potential solution for how to do this.
Sorry I didn't get this part of your answer Just define number of threads available and the output directory. Put this script in your sra file directory and change permission with chmod u+x script. Can you please verify it to me? Thanks Mustafa
@padwalmk provided you with code for a bash script. You will need to put that (in a file say
script.sh) in the directory where you downloaded all.srafiles. You should also change the number that follows--threads 16in script to number of cores you have available on your CPU (if you are using a simple computer locally that number may be 4 or 8). You will also need thegnu parallelprogram (search for it and install if needed). You can then run the bash script by doing something likebash script.shon command prompt.