User aechchiki

17 votes

7 answers

6k views

How to convert BED to GFF3

asked Aug 8, 2017 at 9:59

9 votes

3 answers

3k views

How to convert GFF3 to GTF2

asked Jul 14, 2017 at 13:40

13 votes

2 answers

3k views

How to convert fastq to fast5

asked Aug 15, 2017 at 10:46

7 votes

3 answers

2k views

visualisation of genome alignment

asked Apr 25, 2018 at 8:34

8 votes

2 answers

2k views

estimate genome size: kmer-based approach from PacBio reads

asked Jul 23, 2018 at 7:19

7 votes

1 answer

2k views

STAR-long parameters for aligning RNA ONT reads to genome

asked Aug 30, 2017 at 22:25

4 votes

1 answer

1k views

get gene lines from gtf file

asked May 8, 2018 at 11:13

2 votes

3 answers

1k views

Get start and end coordinates per chromosome

asked Feb 18, 2020 at 9:52

7 votes

1 answer

1k views

Coverage calculation: long reads (RNA-seq)

asked Oct 31, 2017 at 8:15

3 votes

1 answer

865 views

gffread: GFaSeqGet errors on coordinate overhang

asked Feb 27, 2018 at 14:55

5 votes

2 answers

809 views

full visualisation of draft genomes alignment

asked Nov 22, 2018 at 15:02

6 votes

3 answers

496 views

tools to reconcile experimental transcripts with reference annotation

asked Jul 11, 2017 at 7:47

6 votes

1 answer

379 views

PASA pipeline: compare experimental transcripts to the reference annotation

asked Jul 3, 2017 at 9:09

6 votes

1 answer

355 views

Run gffread in multi-thread mode

asked Mar 14, 2018 at 14:21

6 votes

1 answer

323 views

Salmon output: transcripts quantified with zero reads support

asked Mar 12, 2018 at 13:51

9 votes

2 answers

309 views

calling diploid SNVs from long reads

asked Nov 22, 2018 at 10:58

4 votes

2 answers

282 views

Exon-exon junctions: compare experimental transcripts to reference annotation

asked Feb 9, 2018 at 13:40

8 votes

1 answer

279 views

Convert local alignments to spliced alignments in SAM file

asked Aug 30, 2017 at 13:24

3 votes

3 answers

243 views

Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)

asked Dec 3, 2021 at 9:56

0 votes

2 answers

207 views

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

asked Jun 9, 2020 at 16:47

5 votes

1 answer

193 views

Documentation for Transfrag class codes (cuffcompare)

asked Jul 27, 2017 at 12:21

5 votes

1 answer

166 views

Find paralogs in a draft genome

asked Jul 5, 2018 at 10:29

6 votes

1 answer

159 views

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

asked Nov 13, 2017 at 12:10

9 votes

0 answers

141 views

Run cuffcompare in strand-agnostic mode

asked Aug 31, 2017 at 10:26

1 vote

1 answer

106 views

swap genotypes for specific fields of a vcf file

asked Jul 3, 2019 at 13:52

8 votes

4 answers

104 views

Introduce errors in reference transcripts according to external dataset error model

asked Aug 22, 2017 at 16:39

Stack Exchange Network

26 Questions

How to convert BED to GFF3

How to convert GFF3 to GTF2

How to convert fastq to fast5

visualisation of genome alignment

estimate genome size: kmer-based approach from PacBio reads

STAR-long parameters for aligning RNA ONT reads to genome

get gene lines from gtf file

Get start and end coordinates per chromosome

Coverage calculation: long reads (RNA-seq)

gffread: GFaSeqGet errors on coordinate overhang

full visualisation of draft genomes alignment

tools to reconcile experimental transcripts with reference annotation

PASA pipeline: compare experimental transcripts to the reference annotation

Run gffread in multi-thread mode

Salmon output: transcripts quantified with zero reads support

calling diploid SNVs from long reads

Exon-exon junctions: compare experimental transcripts to reference annotation

Convert local alignments to spliced alignments in SAM file

Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)

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

Documentation for Transfrag class codes (cuffcompare)

Find paralogs in a draft genome

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

Run cuffcompare in strand-agnostic mode

swap genotypes for specific fields of a vcf file

Introduce errors in reference transcripts according to external dataset error model