User bli

19 votes

Accepted

How do you write a .gz fastq file with Biopython?

answered Jun 24, 2017 at 6:49

15 votes

How to convert FASTA to BED

answered May 18, 2017 at 11:33

10 votes

Accepted

Understanding DESeq2 design, contrast and results

answered May 22, 2017 at 12:05

8 votes

tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable

answered Jul 6, 2018 at 12:34

7 votes

How to convert fasta file to tab delimited file

answered Oct 19, 2017 at 9:04

7 votes

Are there any databases of templates for common bioinformatic file formats?

answered Jun 2, 2017 at 16:18

7 votes

Accepted

Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?

answered Jul 7, 2017 at 12:58

6 votes

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

answered Jun 2, 2017 at 9:28

6 votes

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

answered Mar 9, 2018 at 12:34

5 votes

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

answered Aug 3, 2018 at 9:25

5 votes

How can I read FCS files using open source libraries?

answered Jun 30, 2017 at 12:51

4 votes

Read length distribution from FASTA file

answered May 18, 2017 at 9:23

4 votes

How do I efficiently subset a very large line-based file?

answered Jun 5, 2017 at 14:17

4 votes

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Output file names are not known beforehand

answered Sep 7, 2018 at 9:30

4 votes

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Group genes by functional categories suming expression values

answered Nov 8, 2018 at 12:08

4 votes

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

answered Mar 21, 2018 at 15:22

4 votes

Automating sequence download from Wormbase

answered Nov 24, 2017 at 12:35

3 votes

Accepted

How can I apply proportional (p) distances (Nucleotide) using bioPython

answered Dec 8, 2017 at 13:16

3 votes

How to create Phylogenetic Trees from fasta files in Python or R?

answered Feb 25, 2019 at 15:55

3 votes

Accepted

Why is 42 the seed used in RunPCA() in Seurat?

answered Jul 9, 2019 at 12:42

3 votes

What is the best way to account for GC-content shift while constructing nucleotide-based phylogenetic tree?

answered May 19, 2017 at 9:18

3 votes

Trying to divide number in fourth TSV column by a certain number according to its corresponding identifier in the first column

answered Feb 26, 2020 at 10:32

3 votes

Suggestion for python graphics library to plot aligned protein sequences

answered Mar 30, 2022 at 20:08

3 votes

To create a new column with Pandas on the basis of two types of column values

answered May 30, 2022 at 10:12

3 votes

Range overlap python error with genomic regions

answered Jun 21, 2017 at 15:27

2 votes

Entrez or Ensembl gene IDs?

answered Jun 7, 2017 at 8:08

2 votes

Subset FASTA file by species name

answered Aug 7, 2017 at 15:06

2 votes

Convert FASTA to FASTQ with dummy quality scores

answered Jan 21, 2020 at 10:39

2 votes

Bash scripting FastQC for multiple fastq files in multiple directories

answered Oct 31, 2018 at 13:33

2 votes

Accepted

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

answered Jul 27, 2018 at 8:52

Stack Exchange Network

41 Answers

How do you write a .gz fastq file with Biopython?

How to convert FASTA to BED

Understanding DESeq2 design, contrast and results

tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable

How to convert fasta file to tab delimited file

Are there any databases of templates for common bioinformatic file formats?

Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

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

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

How can I read FCS files using open source libraries?

Read length distribution from FASTA file

How do I efficiently subset a very large line-based file?

Output file names are not known beforehand

Group genes by functional categories suming expression values

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

Automating sequence download from Wormbase

How can I apply proportional (p) distances (Nucleotide) using bioPython

How to create Phylogenetic Trees from fasta files in Python or R?

Why is 42 the seed used in RunPCA() in Seurat?

What is the best way to account for GC-content shift while constructing nucleotide-based phylogenetic tree?

Trying to divide number in fourth TSV column by a certain number according to its corresponding identifier in the first column

Suggestion for python graphics library to plot aligned protein sequences

To create a new column with Pandas on the basis of two types of column values

Range overlap python error with genomic regions

Entrez or Ensembl gene IDs?

Subset FASTA file by species name

Convert FASTA to FASTQ with dummy quality scores

Bash scripting FastQC for multiple fastq files in multiple directories

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