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 3,191

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

255

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

118

views

Run cuffcompare in strand-agnostic mode

rna-seq transcriptome strandedness

Jul 6 at 14:07 Devon Ryan♦ 18.8k

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 1,971

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

939

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

436

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

326

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

249

views

Run gffread in multi-thread mode

rna-seq fasta file-formats gtf

Mar 14 '18 at 23:30 terdon 7,692

6

votes

1

answer

248

views

Salmon output: transcripts quantified with zero reads support

rna-seq quantification salmon

Mar 12 '18 at 14:06 Devon Ryan♦ 18.8k

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 7,692

2

5

votes

2

answers

565

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

124

views

Find paralogs in a draft genome

genome assembly duplications paralogs

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

5

votes

1

answer

145

views

Documentation for Transfrag class codes (cuffcompare)

transcriptome

Jul 27 '17 at 12:47 Devon Ryan♦ 18.8k

4

votes

1

answer

777

views

get gene lines from gtf file

annotation file-formats gtf

May 8 '18 at 14:16 Devon Ryan♦ 18.8k

4

votes

2

answers

217

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

516

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

353

views

Get start and end coordinates per chromosome

file-formats bed gatk

Apr 7 '20 at 2:47 Geraldine_VdAuwera 380

1

vote

1

answer

77

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

82

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 452

0

votes

0

answers

41

views

merge list of datasets by row IDs in R

r text-processing merge dataframe

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

Stack Exchange Network

current community

your communities

more stack exchange communities

Next badge

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