Running Multiple Flash Sequence Joins in Terminal
I have input files that appear as such:
03631101_1.fastq
03631101_2.fastq
I would like to join the 100+ files I have by running a command in the terminal. From looking at another post, I tried the suggested line:
for i in $(ls *fastq | grep "_1" | cut -f 1 -d "_"); do flash ${i}_1.fastq ${i}_2.fastq; done
But this created an error:
ERROR: zlib error opening
What can I do to create a loop for these fastq files so that I do not have to do each individually?
Thank you!
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Do you want to merge all the
*.fastqfiles into one? If yes, you can usecat.cat *.fastq >> new_file.fastqI would like to create a loop to go through all the fastq files and join them
What OS are you using? Looks like you may be missing the zlib library.
It is OS X Yosemite. I checked and it is already installed.. and updated
Not sure why you are getting a zlib error for a straight for loop. Are there any other files that have a "_1" in name but are not ending in .fastq?
There aren't... but I actually have it working now. The only issue is that the output files come out like out.extendedFrags.fastq and this is being overwritten for each sample number. Do you know what I can add to the end so that the output in a folder called joined takes the sample number from each pair of fastq files? I have tried this for i in $(ls *fastq | grep "_1" | cut -f 1 -d "_"); do flash ${i}_1.fastq ${i}_2.fastq -d joined/-o; done but it just creates the output folder..
Try