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 seperated 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 advices? Thanks a lot!
Thanks a lot Keith!
I downloaded the software and it worked perfectly!
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?
I tried using
seqretsplitto 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?
Please create a new question for this since it is not an answer but another question.