Sequence extract from a big fast file

Question

[vahapel]

Dear All,

After sequencing reaction and extensive filtering, we converted ".fastq" files into ".fasta" files and each fasta file has approximately ~67 million reads. My question is that is there any script for extracting first 30 million reads, then remaining 37 million reads with sequential manner.

Thank you for all your help!

Answer 1

[5heikki]

Assuming no linebreaks in sequences, this is as simple as:

head -n x file > output

Where x is number of seqs times 2 (one line for header, one for sequence). Similarly, you can get the last x sequences utilizing tail.

[vahapel]

Thak you so much, 5heikki. It seems very practical way for such a purpose !

Answer 2

[GouthamAtla]

split fasta file

[vahapel]

Hi, Geek_y, "split fasta file" scripts will be useful for my project, thank you for your help!

[alexandra.lanot]

Hi,

I am a novice using R to split a FASTA file with 300 000 contigs into 6 file of less than 50 000 contigs. I have seen many options but would anyone advise anything that I could be used in R? Thank you A