User aechchiki

15 votes

4 answers

5k 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

1k 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

7 votes

1 answer

1k views

Coverage calculation: long reads (RNA-seq)

asked Oct 31, 2017 at 8:15

2 votes

3 answers

889 views

Get start and end coordinates per chromosome

asked Feb 18, 2020 at 9:52

3 votes

1 answer

728 views

gffread: GFaSeqGet errors on coordinate overhang

asked Feb 27, 2018 at 14:55

5 votes

2 answers

723 views

full visualisation of draft genomes alignment

asked Nov 22, 2018 at 15:02

6 votes

3 answers

473 views

tools to reconcile experimental transcripts with reference annotation

asked Jul 11, 2017 at 7:47

6 votes

1 answer

370 views

PASA pipeline: compare experimental transcripts to the reference annotation

asked Jul 3, 2017 at 9:09

6 votes

1 answer

303 views

Run gffread in multi-thread mode

asked Mar 14, 2018 at 14:21

9 votes

2 answers

292 views

calling diploid SNVs from long reads

asked Nov 22, 2018 at 10:58

6 votes

1 answer

292 views

Salmon output: transcripts quantified with zero reads support

asked Mar 12, 2018 at 13:51

4 votes

2 answers

259 views

Exon-exon junctions: compare experimental transcripts to reference annotation

asked Feb 9, 2018 at 13:40

8 votes

1 answer

256 views

Convert local alignments to spliced alignments in SAM file

asked Aug 30, 2017 at 13:24

5 votes

1 answer

180 views

Documentation for Transfrag class codes (cuffcompare)

asked Jul 27, 2017 at 12:21

0 votes

2 answers

176 views

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

asked Jun 9, 2020 at 16:47

3 votes

3 answers

167 views

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

asked Dec 3, 2021 at 9:56

6 votes

1 answer

158 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

151 views

Find paralogs in a draft genome

asked Jul 5, 2018 at 10:29

9 votes

0 answers

136 views

Run cuffcompare in strand-agnostic mode

asked Aug 31, 2017 at 10:26

8 votes

4 answers

104 views

Introduce errors in reference transcripts according to external dataset error model

asked Aug 22, 2017 at 16:39

1 vote

1 answer

98 views

swap genotypes for specific fields of a vcf file

asked Jul 3, 2019 at 13:52

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

Coverage calculation: long reads (RNA-seq)

Get start and end coordinates per chromosome

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

calling diploid SNVs from long reads

Salmon output: transcripts quantified with zero reads support

Exon-exon junctions: compare experimental transcripts to reference annotation

Convert local alignments to spliced alignments in SAM file

Documentation for Transfrag class codes (cuffcompare)

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

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

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

Find paralogs in a draft genome

Run cuffcompare in strand-agnostic mode

Introduce errors in reference transcripts according to external dataset error model

swap genotypes for specific fields of a vcf file