Hi, I'm looking for an algorithm/code I can use to convert BAM files to bed that I can stick in a C++ file. Preferably something that is generic/works for windows. I'm looking through bedtools but that only works for Unix/Apple so its harder to understand with all the added dependencies and other features bolted on and the inability to build/run it on my system natively (at least without a lot of hassle and additional downloading).
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
If you are not ready to tackle the samtools library (there should be a Windows port, search for it in the forum) and make the BED writer yourself (that part should be simple, though, the BED format isn't that complicated), you could use the Picard library for parsing BAM (in Java, however, and you still need to make a BED writer).
IMHO, I wouldn't start rewriting all the tools to fit them to the platform I use, rather get a platform-independent setup to be able to build and run all tools natively. In your case this means to get a cygwin installation if you only casually need Unix command line tools, or a virtual machine with Linux. I guess BEDtools won't be the only tool made for Unix you'll come across in the near future, if you're working with NGS data...
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
62 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment