User bli

19 votes

2 answers

10k views

Understanding DESeq2 design, contrast and results

asked May 19, 2017 at 14:40

18 votes

2 answers

11k views

How can I extract normalized read count values from DESeq2 results?

asked May 22, 2017 at 14:51

8 votes

5 answers

3k views

Merging bed records based on name

asked Aug 10, 2017 at 12:46

7 votes

1 answer

818 views

What unit do I get on the y-axis of a metagene profile plot?

asked Jun 9, 2017 at 15:08

6 votes

2 answers

2k views

Running differential expression analyses on count matrices with many zeroes

asked Jun 26, 2017 at 9:14

6 votes

1 answer

273 views

What is this 5-column sequencing format from 2009?

asked Oct 31, 2017 at 14:58

6 votes

2 answers

555 views

Same transcript coordinates in gtf file, different transcript ID

asked Jul 25, 2017 at 15:56

6 votes

1 answer

715 views

Using pysam with cython: htslib/kstring.h not found

asked Aug 2, 2018 at 17:36

5 votes

2 answers

3k views

How can I easily get the read size distribution of reads mapping on a certain set of regions?

asked Mar 21, 2018 at 15:22

5 votes

1 answer

185 views

Dealing with absence of coverage

asked Sep 14, 2017 at 9:24

5 votes

1 answer

490 views

Customizing bigWig file

asked Jun 13, 2017 at 17:07

4 votes

1 answer

339 views

What kind of "gff" format does bioawk parse?

asked Jun 12, 2017 at 15:30

4 votes

1 answer

354 views

Adding entries to bigwig file

asked Oct 30, 2017 at 10:39

4 votes

1 answer

279 views

How can I reproduce a manual NCBI search with Biopython Entrez module?

asked Mar 9, 2018 at 12:23

3 votes

1 answer

66 views

Automating sequence download from Wormbase

asked Nov 24, 2017 at 12:35

3 votes

1 answer

2k views

Counts obtained by featureCounts seem much less than observed coverage

asked Jul 19, 2017 at 13:41

3 votes

1 answer

99 views

Detecting broad peaks in sRNA-seq data

asked Jun 7, 2019 at 16:51

1 vote

1 answer

82 views

How to detect bedtools version used by pybedtools (in order to correctly preserve strand information when merging gtf records)

asked Apr 30, 2021 at 8:07

1 vote

1 answer

178 views

How to efficiently extract coordinates from a `pybedtools.Interval`?

asked Jul 27, 2018 at 8:52

1 vote

4 answers

425 views

At what processing step should library strandedness type be taken into account?

asked Jul 18, 2017 at 13:26

0 votes

2 answers

328 views

Filtering bam file with bedtools intersect using strand specificity

asked Apr 12, 2018 at 15:52

Stack Exchange Network

21 Questions

Understanding DESeq2 design, contrast and results

How can I extract normalized read count values from DESeq2 results?

Merging bed records based on name

What unit do I get on the y-axis of a metagene profile plot?

Running differential expression analyses on count matrices with many zeroes

What is this 5-column sequencing format from 2009?

Same transcript coordinates in gtf file, different transcript ID

Using pysam with cython: htslib/kstring.h not found

How can I easily get the read size distribution of reads mapping on a certain set of regions?

Dealing with absence of coverage

Customizing bigWig file

What kind of "gff" format does bioawk parse?

Adding entries to bigwig file

How can I reproduce a manual NCBI search with Biopython Entrez module?

Automating sequence download from Wormbase

Counts obtained by featureCounts seem much less than observed coverage

Detecting broad peaks in sRNA-seq data

How to detect bedtools version used by pybedtools (in order to correctly preserve strand information when merging gtf records)

How to efficiently extract coordinates from a `pybedtools.Interval`?

At what processing step should library strandedness type be taken into account?

Filtering bam file with bedtools intersect using strand specificity