User aechchiki

15 votes

4 answers

4k 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

software-recommendation format-conversion gff3 gtf

asked Jul 14, 2017 at 13:40

13 votes

2 answers

2k views

How to convert fastq to fast5

nanopore software-recommendation fastq format-conversion fast5

asked Aug 15, 2017 at 10:46

7 votes

3 answers

2k views

visualisation of genome alignment

alignment software-recommendation mauve

asked Apr 25, 2018 at 8:34

8 votes

2 answers

1k views

estimate genome size: kmer-based approach from PacBio reads

genome software-recommendation assembly k-mer pacbio

asked Jul 23, 2018 at 7:19

6 votes

1 answer

1k views

STAR-long parameters for aligning RNA ONT reads to genome

nanopore rna-alignment star gmap

asked Aug 30, 2017 at 22:25

7 votes

1 answer

1k views

Coverage calculation: long reads (RNA-seq)

rna-seq transcriptome long-reads pacbio coverage

asked Oct 31, 2017 at 8:15

4 votes

1 answer

995 views

get gene lines from gtf file

annotation file-formats gtf

asked May 8, 2018 at 11:13

5 votes

2 answers

672 views

full visualisation of draft genomes alignment

sequence-alignment genome software-recommendation visualization

asked Nov 22, 2018 at 15:02

3 votes

1 answer

626 views

gffread: GFaSeqGet errors on coordinate overhang

rna-seq alignment software-recommendation base-clipping

asked Feb 27, 2018 at 14:55

2 votes

3 answers

619 views

Get start and end coordinates per chromosome

file-formats bed gatk

asked Feb 18, 2020 at 9:52

6 votes

3 answers

457 views

tools to reconcile experimental transcripts with reference annotation

alignment transcriptome software-recommendation

asked Jul 11, 2017 at 7:47

6 votes

1 answer

358 views

PASA pipeline: compare experimental transcripts to the reference annotation

rna-seq assembly transcriptome isoform

asked Jul 3, 2017 at 9:09

6 votes

1 answer

276 views

Run gffread in multi-thread mode

rna-seq fasta file-formats gtf

asked Mar 14, 2018 at 14:21

9 votes

2 answers

275 views

calling diploid SNVs from long reads

vcf snp variant-calling long-reads pacbio

asked Nov 22, 2018 at 10:58

6 votes

1 answer

270 views

Salmon output: transcripts quantified with zero reads support

rna-seq quantification salmon

asked Mar 12, 2018 at 13:51

8 votes

1 answer

243 views

Convert local alignments to spliced alignments in SAM file

sam rna-alignment rna-splicing

asked Aug 30, 2017 at 13:24

4 votes

2 answers

239 views

Exon-exon junctions: compare experimental transcripts to reference annotation

rna-seq software-recommendation rna-splicing

asked Feb 9, 2018 at 13:40

5 votes

1 answer

160 views

Documentation for Transfrag class codes (cuffcompare)

transcriptome

asked Jul 27, 2017 at 12:21

6 votes

1 answer

155 views

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

proteins assembly validation

asked Nov 13, 2017 at 12:10

0 votes

2 answers

138 views

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

r text-processing merge

asked Jun 9, 2020 at 16:47

5 votes

1 answer

131 views

Find paralogs in a draft genome

genome assembly duplications paralogs

asked Jul 5, 2018 at 10:29

9 votes

0 answers

129 views

Run cuffcompare in strand-agnostic mode

rna-seq transcriptome strandedness

asked Aug 31, 2017 at 10:26

3 votes

2 answers

105 views

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

phylogenetics annotation covid-19 sars-cov-2 variants

asked Dec 3, 2021 at 9:56

8 votes

4 answers

102 views

Introduce errors in reference transcripts according to external dataset error model

rna-seq software-recommendation nanopore simulated-data

asked Aug 22, 2017 at 16:39

1 vote

1 answer

91 views

swap genotypes for specific fields of a vcf file

vcf file-formats variant-calling text-processing

asked Jul 3, 2019 at 13:52

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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

Coverage calculation: long reads (RNA-seq)

get gene lines from gtf file

full visualisation of draft genomes alignment

gffread: GFaSeqGet errors on coordinate overhang

Get start and end coordinates per chromosome

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

Convert local alignments to spliced alignments in SAM file

Exon-exon junctions: compare experimental transcripts to reference annotation

Documentation for Transfrag class codes (cuffcompare)

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

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

Find paralogs in a draft genome

Run cuffcompare in strand-agnostic mode

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

Introduce errors in reference transcripts according to external dataset error model

swap genotypes for specific fields of a vcf file