Hi All,
I need to split my fastq file that is composed of 30 chromosomes into 30 different files containing each the information from one chromosome. Technically, I need to split this kind of file into separated one:
@chr1
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgctgggtgatctttagtcnnnnnnnnnn
nnnnnnnnnnnnnnnnatggggtcatgtacacacacacattggatannnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgctgggtgatctttagtcnnnnnnnnnn
..
@chr2
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgctgggtgatctttagtcnnnnnnnnnn
nnnnnnnnnnnnnnnnatggggtcatgtacacacacacattggatannnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgctgggtgatctttagtcnnnnnnnnnn
..
I tried to use:
awk '/^@chr1$/,/^+$/' consensus.fastq | perl -pe "s/@/>/ ; s/\+//" > chr1.fasta
but that gives me this:
@chr1
nnnnnagtnnnnnnnnnnnnnnnnnnnnnttgcnnnnnnnnnnnnnnnnnnnnnngcnnn
nnnntgaaannnnnnnnnnnntcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
Did somebody had already this kind of problems? Could somebody gives me some advice?
Thanks a lot!
Nath
Thanks a lot Keith!
I downloaded the software and it worked perfectly!
Cheers, Nath
Nath, you should have appended this as a comment to the previous question rather than as a separate answer. If Keith's answer is spot on for you, consider checking the tick box on his answer, so that this becomes the 'accepted answer'.
Isn't it a little harsh to downvote a new user with a rep of 19 for an honest mistake?
Ok, thanks Daniel! Sorry, it is the first time I used this kind of forum. Thank a lot for your advice! Nath
I know it is old post, but what was the software used?
Hi ALL,
I tried using
seqretsplit
to split a fastq file because I do not have enough memory to load the entire file into fastq. I used:However, the number of output files were as many as the number sequences. Is there any flag which can be used to specify how many files and therefore how many sequences would each file contain?
Many thanks
Please create a new question for this since it is not an answer but another question.