Thank you! That's solved it!
• 0 views
•
link
written
by
sendhelp •
Filter nanopore fastq files by start time
Hi,
I have a set of nanopore fastq files with headers in the following format:
@29d30612-b8b4-4ab5-967f-531fc2851541 runid=0a82096db062bcf8041358b407ab5e0aa5de7138 read=23606 ch=186 start_time=2019-03-11T16:16:33Z flow_cell_id= protocol_group_id=190311_ang_1 sample_id=190311_ang_1 TCAGTGTACTTCGTTCAATCGCGTTTTCGTGCGCTTTCAGCAAATCTGCCTCACCTCTCCTCTCCACA
I'd like to filter through the fastq reads and extract only those reads that occured in a given time period (e.g. the first hour). I've tried using poretools --end function but can't work out the correct format of the timestamp to use. Any help would be much appreciated, either with the correct format for poretools or a command that would enable me to do this!
Thanks!
• 3,691 views
•
link
updated
by
zhanxw •
•
written
by
sendhelp •
•
written
by
sendhelp •
3 answers
There are a couple of solutions in this thread: Extract fastq sequences based on date/time (which is in the header)
You might try a grep and include the following three lines (as FASTQ contains four lines per read.
So if you want data from 1600-1659 try
grep -A3 "2019-03-11T16" x.fastq > test.fastq
Then to see how many reads you filtered out
wc -l x.fastq
wc -l test.fastq
Check the format is ok too
head test.fastq
Not tested, but the approach may still work :-)
• 0 views
•
link
written
by
colindaven
I found a python script from the link below that works well so haven't tried this but thank you for the help!
• 0 views
•
link
written
by
sendhelp •
This is an efficient tool: https://github.com/angelovangel/nanotimes
Log in to answer this question.
More posts like this
