User aechchiki

15 votes

4 answers

5k views

How to convert BED to GFF3

asked Aug 8, 2017 at 9:59

13 votes

2 answers

3k views

How to convert fastq to fast5

asked Aug 15, 2017 at 10:46

9 votes

0 answers

136 views

Run cuffcompare in strand-agnostic mode

asked Aug 31, 2017 at 10:26

9 votes

3 answers

3k views

How to convert GFF3 to GTF2

asked Jul 14, 2017 at 13:40

9 votes

2 answers

288 views

calling diploid SNVs from long reads

asked Nov 22, 2018 at 10:58

8 votes

2 answers

2k views

estimate genome size: kmer-based approach from PacBio reads

asked Jul 23, 2018 at 7:19

8 votes

4 answers

104 views

Introduce errors in reference transcripts according to external dataset error model

asked Aug 22, 2017 at 16:39

8 votes

1 answer

254 views

Convert local alignments to spliced alignments in SAM file

asked Aug 30, 2017 at 13:24

7 votes

1 answer

1k views

STAR-long parameters for aligning RNA ONT reads to genome

asked Aug 30, 2017 at 22:25

7 votes

1 answer

1k views

Coverage calculation: long reads (RNA-seq)

asked Oct 31, 2017 at 8:15

7 votes

3 answers

2k views

visualisation of genome alignment

asked Apr 25, 2018 at 8:34

6 votes

1 answer

366 views

PASA pipeline: compare experimental transcripts to the reference annotation

asked Jul 3, 2017 at 9:09

6 votes

3 answers

470 views

tools to reconcile experimental transcripts with reference annotation

asked Jul 11, 2017 at 7:47

6 votes

1 answer

290 views

Salmon output: transcripts quantified with zero reads support

asked Mar 12, 2018 at 13:51

6 votes

1 answer

300 views

Run gffread in multi-thread mode

asked Mar 14, 2018 at 14:21

6 votes

1 answer

157 views

Verify a predicted protein in one genome in a different genome of the same species

asked Nov 13, 2017 at 12:10

5 votes

1 answer

147 views

Find paralogs in a draft genome

asked Jul 5, 2018 at 10:29

5 votes

1 answer

173 views

Documentation for Transfrag class codes (cuffcompare)

asked Jul 27, 2017 at 12:21

5 votes

2 answers

715 views

full visualisation of draft genomes alignment

asked Nov 22, 2018 at 15:02

4 votes

1 answer

1k views

get gene lines from gtf file

asked May 8, 2018 at 11:13

4 votes

2 answers

254 views

Exon-exon junctions: compare experimental transcripts to reference annotation

asked Feb 9, 2018 at 13:40

3 votes

1 answer

687 views

gffread: GFaSeqGet errors on coordinate overhang

asked Feb 27, 2018 at 14:55

3 votes

2 answers

135 views

Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

asked Dec 3, 2021 at 9:56

2 votes

3 answers

826 views

Get start and end coordinates per chromosome

asked Feb 18, 2020 at 9:52

1 vote

1 answer

97 views

swap genotypes for specific fields of a vcf file

asked Jul 3, 2019 at 13:52

0 votes

2 answers

173 views

merge rows (to columns) in R dataframe based on IDs

asked Jun 9, 2020 at 16:47

Stack Exchange Network

26 Questions

How to convert BED to GFF3

How to convert fastq to fast5

Run cuffcompare in strand-agnostic mode

How to convert GFF3 to GTF2

calling diploid SNVs from long reads

estimate genome size: kmer-based approach from PacBio reads

Introduce errors in reference transcripts according to external dataset error model

Convert local alignments to spliced alignments in SAM file

STAR-long parameters for aligning RNA ONT reads to genome

Coverage calculation: long reads (RNA-seq)

visualisation of genome alignment

PASA pipeline: compare experimental transcripts to the reference annotation

tools to reconcile experimental transcripts with reference annotation

Salmon output: transcripts quantified with zero reads support

Run gffread in multi-thread mode

Verify a predicted protein in one genome in a different genome of the same species

Find paralogs in a draft genome

Documentation for Transfrag class codes (cuffcompare)

full visualisation of draft genomes alignment

get gene lines from gtf file

Exon-exon junctions: compare experimental transcripts to reference annotation

gffread: GFaSeqGet errors on coordinate overhang

Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

Get start and end coordinates per chromosome

swap genotypes for specific fields of a vcf file

merge rows (to columns) in R dataframe based on IDs