User aechchiki

12

votes

2

answers

2k

views

How to convert fastq to fast5

Nov 2 '18 at 12:22 Michael Hall 563

1

12

votes

4

answers

4k

views

How to convert BED to GFF3

software-recommendation bed format-conversion gff3

Aug 10 '17 at 13:39 Ian Sudbery 3,181

1

9

votes

3

answers

2k

views

How to convert GFF3 to GTF2

software-recommendation format-conversion gff3 gtf

Jul 9 at 10:13 juke34 113

1

9

votes

2

answers

254

views

calling diploid SNVs from long reads

vcf snp variant-calling long-reads pacbio

Feb 21 '19 at 10:18 user4162 36

8

votes

0

answers

117

views

Run cuffcompare in strand-agnostic mode

rna-seq transcriptome strandedness

Jul 6 at 14:07 Devon Ryan♦ 18.7k

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

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 1,931

8

votes

4

answers

99

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 5,441

7

votes

1

answer

933

views

Coverage calculation: long reads (RNA-seq)

rna-seq transcriptome long-reads pacbio coverage

Apr 15 '19 at 16:58 Glorfindel 153

1

7

votes

3

answers

2k

views

visualisation of genome alignment

alignment software-recommendation mauve

Apr 26 '18 at 15:24 aechchiki 2,514

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♦ 10.6k

1

6

votes

3

answers

430

views

tools to reconcile experimental transcripts with reference annotation

alignment transcriptome software-recommendation

Apr 10 '18 at 23:42 gringer♦ 10.6k

6

votes

1

answer

322

views

PASA pipeline: compare experimental transcripts to the reference annotation

rna-seq assembly transcriptome isoform

Apr 10 '18 at 7:44 aechchiki 2,514

6

votes

1

answer

238

views

Run gffread in multi-thread mode

rna-seq fasta file-formats gtf

Mar 14 '18 at 23:30 terdon 7,505

6

votes

1

answer

240

views

Salmon output: transcripts quantified with zero reads support

rna-seq quantification salmon

Mar 12 '18 at 14:06 Devon Ryan♦ 18.7k

6

votes

1

answer

151

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 7,505

2

5

votes

2

answers

552

views

full visualisation of draft genomes alignment

sequence-alignment genome software-recommendation visualization

Nov 26 '18 at 7:28 aechchiki 2,514

5

votes

1

answer

121

views

Find paralogs in a draft genome

genome assembly duplications paralogs

Jul 9 '18 at 4:48 conchoecia 2,922

5

votes

1

answer

143

views

Documentation for Transfrag class codes (cuffcompare)

transcriptome

Jul 27 '17 at 12:47 Devon Ryan♦ 18.7k

4

votes

1

answer

756

views

get gene lines from gtf file

annotation file-formats gtf

May 8 '18 at 14:16 Devon Ryan♦ 18.7k

4

votes

2

answers

215

views

Exon-exon junctions: compare experimental transcripts to reference annotation

rna-seq software-recommendation rna-splicing

Feb 12 '18 at 14:52 user172818 5,441

3

votes

1

answer

504

views

gffread: GFaSeqGet errors on coordinate overhang

rna-seq alignment software-recommendation base-clipping

Feb 27 '18 at 14:55 aechchiki 2,514

2

votes

3

answers

330

views

Get start and end coordinates per chromosome

file-formats bed gatk

Apr 7 '20 at 2:47 Geraldine_VdAuwera 370

1

vote

1

answer

74

views

swap genotypes for specific fields of a vcf file

vcf file-formats variant-calling text-processing

Jul 4 '19 at 11:51 aechchiki 2,514

0

votes

2

answers

78

views

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

r text-processing merge

Jun 10 '20 at 5:25 thomas duge de bernonville 442

0

votes

0

answers

40

views

merge list of datasets by row IDs in R

r text-processing merge dataframe

Jun 9 '20 at 16:57 aechchiki 2,514

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26 Questions

How to convert fastq to fast5

How to convert BED to GFF3

How to convert GFF3 to GTF2

calling diploid SNVs from long reads

Run cuffcompare in strand-agnostic mode

estimate genome size: kmer-based approach from PacBio reads

Convert local alignments to spliced alignments in SAM file

Introduce errors in reference transcripts according to external dataset error model

Coverage calculation: long reads (RNA-seq)

visualisation of genome alignment

STAR-long parameters for aligning RNA ONT reads to genome

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

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

full visualisation of draft genomes alignment

Find paralogs in a draft genome

Documentation for Transfrag class codes (cuffcompare)

get gene lines from gtf file

Exon-exon junctions: compare experimental transcripts to reference annotation

gffread: GFaSeqGet errors on coordinate overhang

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

merge list of datasets by row IDs in R