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3.0 years ago
dahun73
▴
10
Hello All,
I have a question about fragment length while drawing coverage plot. Normally, many software have an option to adjust "fragment length". But I'm confused if it is paired-end. if each length of fastq is 75bp, fragment length is 150bp, right? Because same named reads of R1 and R2 are aligned.
Thank you in advance!
my understanding is that the fragment length is the length of the bit of DNA/RNA where the R1 and R2 reads are the either end of it. fragment length is thus linked to the fragmentation (and size selection) done on your input material. Usually this is in the 400-500 nucleotide range.
here is some more insight in this: Insert Size And Fragment Size ?
thank you for reply!
Then, should I set the fragment length option to 400~500? In my experience, coverage plot was extended when I extended the fragment length. So, I'm curious whether 'the fragment length' is only from library preparation. Or, is there any other meaning for "fragment length" of coverage plot tool?
the 4-500 range i mentioned was merely an example. You should look up in with the sequencing facility (or the metadata) what the used fragment length was for your data.
Well, this terminology is not strict determined. sometimes people will interpret this as the "insert length" (== the bit of sequence between R1 and R2, "the gap" ) .... so it's key to see what measure the tool you plan to use is using.