User: Click downvote
Click downvote • 650
- Reputation:
- 650
- Status:
- Trusted
- Location:
- Germany
- Last seen:
- 2 months, 4 weeks ago
- Joined:
- 6 years, 3 months ago
- Email:
- e*********@gmail.com
Posts by Click downvote
<prev
• 137 results •
page 1 of 14 •
next >
0
votes
1
answer
225
views
1
answers
... Thanks, will start to read up on it. ...
written 3 months ago by
Click downvote • 650
0
votes
1
answer
225
views
1
answers
... It is a reimplementation of a very popular piece of software. It is already working well, I am just irked that reading bam takes 3x as long as bed reading. ...
written 3 months ago by
Click downvote • 650
0
votes
1
answer
225
views
1
answers
... Getting the start, len, strand and reference. It is for a ChIP-Seq caller :) ...
written 3 months ago by
Click downvote • 650
8
votes
1
answer
225
views
5 follow
1
answer
... This is a tiny script that is enough to get gcc to fail when trying to build:
#include
#include
#include
#include
int main(int argc, char *argv[]){
samFile *fp_in = hts_open(argv[1],"r"); //open bam file
bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //re ...
written 3 months ago by
Click downvote • 650
• updated
3 months ago by
John Marshall • 1.5k
0
votes
2
answers
237
views
2
answers
... I just need to stream the file. I guess the error is on my part as I have not used C much, just Cython. ...
written 3 months ago by
Click downvote • 650
0
votes
2
answers
237
views
2
answers
... But I have the htslib conda installed and still #include errors. I think I will just use pysam, but give a warning that it is slower than the C++ bed reader. ...
written 3 months ago by
Click downvote • 650
0
votes
2
answers
237
views
2
answers
... But I am using cython. How can I use compile flags to point to the system installation of htslib? Users have no way to point to an installed version when `pip installing` my library. ...
written 3 months ago by
Click downvote • 650
2
votes
2
answers
237
views
2
answers
... I will submit to all of your expertise. Added htslib in a lib folder in my project. ...
written 3 months ago by
Click downvote • 650
0
votes
2
answers
237
views
2
answers
... But pysam is slow as each record is a Python object which needs to be parsed. ...
written 3 months ago by
Click downvote • 650
0
votes
2
answers
237
views
2
answers
... MACS2 seems to be able to read bam without any special utilities: https://github.com/taoliu/MACS/blob/33187eae605081c8ddad9313a886bd01d2c654cd/MACS2/IO/Parser.pyx#L732
However, I do not know if the code is brittle, or especially fast. It used the struct library so it cannot be compiled down to pure ...
written 3 months ago by
Click downvote • 650
Latest awards to Click downvote
Scholar
3 months ago,
created an answer that has been accepted.
For C: Is there a single header file somewhere I can use to read bam?
Great Question
7 months ago,
created a question with more than 5,000 views.
For Why Aren'T Guide Trees (Necessarily) Phylogenetic Trees?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For What Are The Files Named "Random" In Genome Sequences?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Bioinformatics: How To Version Control Small Scripts Located All Over The Server.
Great Question
9 months ago,
created a question with more than 5,000 views.
For Why Aren'T Guide Trees (Necessarily) Phylogenetic Trees?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Should You Combine Ontologies In Gohypergparams? If So, How?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Clustalw: Why Is It Bad That Many Similar Sequences Dominate The Alignment Score?
Great Question
2.7 years ago,
created a question with more than 5,000 views.
For Converting Tped To Ped
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Bioinformatics: How To Version Control Small Scripts Located All Over The Server.
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Should Bowtie Hits On Negative Strand Be Counted Downwards To Find The End Of The Alignment (Illustrated)?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Representing Short Read Clusters As Feature Vectors- Which Properties To Include?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Why Aren'T Guide Trees (Necessarily) Phylogenetic Trees?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For How To Find Out Whether There Is A Statistical Difference Between Two Sets Of Strings?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Bowtie Outputs Hits That Are Shorter Than The Reads Aligned
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Computing Similarity Between Lists Of Enriched Terms
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Creating Reads With Same Nucleotides And Dinucleotides- I.E. Scrambling Reads
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Collapse Reads That Are Substrings Of Other Reads In Same Library
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Using Bowtie To Only Search In Restricted Regions
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Finding Mirna Seed Region By Aligning Mirna And Seeing That Positions 2-8 Hit Fewer Snps
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For What Does It Mean That Blosum Does Not Model Real Substitutions (As Opposed To Say Pam?)
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Where To Find Libraries/Read Files Of All Rnas Found In A Cell
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Best Python Support Vector Machine Implementation For Bioinformatics (Classifying Short Reads)?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For How Do I Find The Number Of Individuals In A Vcf File?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For How To Tell If Bed/Bim/Fam Data Are Phased?
Great Question
2.7 years ago,
created a question with more than 5,000 views.
For Data Too Big To Be Stored In Memory: Common Options
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1120 users visited in the last hour