Self-ligated and undigested fragments

[tlgolan]

Hi, In order to remove the above fragments, I found the primer's fragment (the fragment containing the primer) and remove the adjacent fragments, before and after it. Is it an acceptable way? Thanks

[rr1859]

You are removing the fragments before and after from just the observed fragments? It should be ok - but you are making the assumption that the self-ligated and undigested fragment is unique and that it has observed fragments. In some cases these fragments can be repetitive and therefore you cannot map reads to it. To be sure I would get the coordinates for these fragments from the original fragment file (before removing duplicated sequences)

[tlgolan]

I just want to make myself clear: this is a partial fragment file (fragment number, chr, start, end, counts):

50573 chr5 164788441 164790436 8703 50574 chr5 164790443 164793939 141840
50575 chr5 164793946 164799104 120491

fragment number 50574 is the fragment containing the primer (and also the bait). I removed fragment number 50573 ('before fragment') and fragment number 50575 ('after fragment'). Does it change your opinion? I believe not because this adjacent fragments contain reads. Thanks a lot for your help!

[rr1859]

Ok - in your case it should be fine to do that.