I found one data of my interest from SRA. But the file is too big.
Is it possible to obtain specific reads from SRA (preferably) based on sequence string of my gene or region of interest?
Also if it is possible to do it with fastq file would be manageable?
Basically I want to avoid aligning full data which could be time-consuming and memory intensive. So I want to focus only reads of my interest.
I tried seqtk but it require read name and I don't know which read name to take.
grepping the sequence is another option but I would lose fastq based information
That's why I am looking for tools based on read subset/seed sequence. eg. AAATTCGC
I would appreciate any help.
In case if somebody else want to do similar things, the command could be as follows:
where k is the length of sequence
kwould get full length sequences. If you need to get partial matches then
kshould be set to less than 1/2 length of pattern one is searching for.