Timeline for Why do we delete scaffolds shorter than 500 - 1000 bp from the assembled genome?
Current License: CC BY-SA 4.0
6 events
| when toggle format | what | by | license | comment | |
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| Oct 9, 2023 at 0:36 | comment | added | Ammar | Agree with what @rainman has said. depending on the organism, you might want to go lower, eg if the genome is is tiny you might drop the cutoff. Also it's good to note there are scaffolding tools that help bridge the gap between contigs. | |
| Oct 6, 2023 at 19:20 | comment | added | Rainman | Oh and for the cutoffs: I work with metagenomes, so I tend to work my cutoff around my assembly N50. Say the N50 is 2100, I will round that to 2000 and remove any scaffolds smaller than that. It seems to help me save the majority of the data whilst minimizing noise. Each case will be different though :) | |
| S Oct 6, 2023 at 18:11 | review | First answers | |||
| Oct 11, 2023 at 8:09 | |||||
| S Oct 6, 2023 at 18:11 | history | edited | Rainman | CC BY-SA 4.0 |
deleted 2 characters in body
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| S Oct 6, 2023 at 17:08 | review | First answers | |||
| Oct 6, 2023 at 17:57 | |||||
| S Oct 6, 2023 at 17:08 | history | answered | Rainman | CC BY-SA 4.0 |