So far, I have tried the following python packges and they all have caused me to run out of RAM and are not as efficient as I would like: pysam, pyfaidx, SeqIO.
I have a df with milliions of coordinates that I need the sequences for, but I am unsure how I can do this without reaching the RAM limit. Would bedtools help if I use the terminal?
Any suggestions would be greatly appreciated.
1 answer
I'm not very familiar, but I have to imagine the command line should be able to do this easily. Maybe depends on size of your regions, but bedtools or samtools should work for you.
I did a test with 4G of RAM (allocated on HPC) and 5.6 million regions (repetitions of mm10 gene gtf). Took a few minutes, but bedtools and samtools ran without issue. Resulting fasta was 17G.
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