Bedtools documentation states that one can add two extra fields to a bedpe file when using bamtobed. Does anyone know how to do that? I need to add the read sequences. Thanks.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
one possible solution is to use your bed output in conjunction with
bedtools getfasta -tab
then parse the output to get the bed formatting back by perl -wpl -i.bak -e 's/:|-/\t/g;'
if you need the reads themselves and not the genome sequence where they mapped, you could write a sam parser to simply print some of the columns of the sam file. all the info you need is in the sam, just need to look at the sam docs to figure out what you want to print (i.e. which columns) and how to modify the sam to get bed-like coordinates. awk is good for such a task, just be aware of the strand
Latest Articles
Collapse
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
-
by seqadmin
Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...-
Channel: Articles
02-26-2024, 02:07 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 03-14-2024, 06:13 AM
|
0 responses
34 views
0 likes
|
Last Post
by seqadmin
03-14-2024, 06:13 AM
|
||
Started by seqadmin, 03-08-2024, 08:03 AM
|
0 responses
72 views
0 likes
|
Last Post
by seqadmin
03-08-2024, 08:03 AM
|
||
Started by seqadmin, 03-07-2024, 08:13 AM
|
0 responses
81 views
0 likes
|
Last Post
by seqadmin
03-07-2024, 08:13 AM
|
||
Started by seqadmin, 03-06-2024, 09:51 AM
|
0 responses
68 views
0 likes
|
Last Post
by seqadmin
03-06-2024, 09:51 AM
|
Comment