User aechchiki

1

12

votes

4

answers

4k

views

How to convert BED to GFF3

Aug 10 '17 at 13:39 Ian Sudbery 3,191

1

9

votes

3

answers

3k

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How to convert GFF3 to GTF2

software-recommendation format-conversion gff3 gtf

Jul 9 at 10:13 juke34 113

12

votes

2

answers

2k

views

How to convert fastq to fast5

nanopore software-recommendation fastq format-conversion fast5

Nov 2 '18 at 12:22 Michael Hall 563

1

7

votes

3

answers

2k

views

visualisation of genome alignment

alignment software-recommendation mauve

Apr 26 '18 at 15:24 aechchiki 2,524

2

8

votes

2

answers

1k

views

estimate genome size: kmer-based approach from PacBio reads

genome software-recommendation assembly k-mer pacbio

Apr 19 '20 at 18:34 Tane 31

6

votes

1

answer

1k

views

STAR-long parameters for aligning RNA ONT reads to genome

nanopore rna-alignment star gmap

Feb 22 '19 at 22:54 gringer♦ 10.8k

7

votes

1

answer

952

views

Coverage calculation: long reads (RNA-seq)

rna-seq transcriptome long-reads pacbio coverage

Apr 15 '19 at 16:58 Glorfindel 153

4

votes

1

answer

788

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get gene lines from gtf file

annotation file-formats gtf

May 8 '18 at 14:16 Devon Ryan♦ 18.9k

2

5

votes

2

answers

582

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full visualisation of draft genomes alignment

sequence-alignment genome software-recommendation visualization

Nov 26 '18 at 7:28 aechchiki 2,524

3

votes

1

answer

523

views

gffread: GFaSeqGet errors on coordinate overhang

rna-seq alignment software-recommendation base-clipping

Feb 27 '18 at 14:55 aechchiki 2,524

1

6

votes

3

answers

440

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tools to reconcile experimental transcripts with reference annotation

alignment transcriptome software-recommendation

Apr 10 '18 at 23:42 gringer♦ 10.8k

2

votes

3

answers

394

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Get start and end coordinates per chromosome

file-formats bed gatk

Apr 7 '20 at 2:47 Geraldine_VdAuwera 380

6

votes

1

answer

329

views

PASA pipeline: compare experimental transcripts to the reference annotation

rna-seq assembly transcriptome isoform

Apr 10 '18 at 7:44 aechchiki 2,524

1

9

votes

2

answers

257

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calling diploid SNVs from long reads

vcf snp variant-calling long-reads pacbio

Feb 21 '19 at 10:18 user4162 36

6

votes

1

answer

253

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Run gffread in multi-thread mode

rna-seq fasta file-formats gtf

Mar 14 '18 at 23:30 terdon 7,772

6

votes

1

answer

253

views

Salmon output: transcripts quantified with zero reads support

rna-seq quantification salmon

Mar 12 '18 at 14:06 Devon Ryan♦ 18.9k

4

votes

2

answers

221

views

Exon-exon junctions: compare experimental transcripts to reference annotation

rna-seq software-recommendation rna-splicing

Feb 12 '18 at 14:52 user172818 5,451

8

votes

1

answer

218

views

Convert local alignments to spliced alignments in SAM file

sam rna-alignment rna-splicing

Nov 18 '18 at 8:35 winni2k 1,981

6

votes

1

answer

152

views

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

proteins assembly validation

Nov 13 '17 at 20:10 terdon 7,772

5

votes

1

answer

145

views

Documentation for Transfrag class codes (cuffcompare)

transcriptome

Jul 27 '17 at 12:47 Devon Ryan♦ 18.9k

5

votes

1

answer

124

views

Find paralogs in a draft genome

genome assembly duplications paralogs

Jul 9 '18 at 4:48 conchoecia 3,011

8

votes

0

answers

120

views

Run cuffcompare in strand-agnostic mode

rna-seq transcriptome strandedness

Jul 6 at 14:07 Devon Ryan♦ 18.9k

8

votes

4

answers

100

views

Introduce errors in reference transcripts according to external dataset error model

rna-seq software-recommendation nanopore simulated-data

Aug 25 '17 at 12:23 user172818 5,451

0

votes

2

answers

85

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

r text-processing merge

Jun 10 '20 at 5:25 thomas duge de bernonville 452

1

vote

1

answer

82

views

swap genotypes for specific fields of a vcf file

vcf file-formats variant-calling text-processing

Jul 4 '19 at 11:51 aechchiki 2,524

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25 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

tools to reconcile experimental transcripts with reference annotation

Get start and end coordinates per chromosome

PASA pipeline: compare experimental transcripts to the reference annotation

calling diploid SNVs from long reads

Run gffread in multi-thread mode

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

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

Documentation for Transfrag class codes (cuffcompare)

Find paralogs in a draft genome

Run cuffcompare in strand-agnostic mode

Introduce errors in reference transcripts according to external dataset error model

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

swap genotypes for specific fields of a vcf file