User aechchiki

8 votes

Extracting expression data from GSE dataset downloaded from GEO

answered Aug 30, 2017 at 9:30

6 votes

What format is this? Pretty sure it's not a BED file

answered Aug 29, 2017 at 17:45

6 votes

Accepted

Cufflinks Error: sort order of reads in BAMs must be the same

answered Apr 3, 2018 at 12:18

6 votes

Accepted

full visualisation of draft genomes alignment

answered Nov 23, 2018 at 10:32

5 votes

Accepted

How to measure the total size of a fastq file in base pairs?

answered Sep 1, 2020 at 13:17

5 votes

Converting a BAM file into VCF

answered Apr 8, 2018 at 14:21

5 votes

Accepted

Salmon tximport

answered Apr 9, 2018 at 9:29

4 votes

Accepted

visualisation of genome alignment

answered Apr 26, 2018 at 15:24

4 votes

Is there a way to quickly verify the presence of some SNPs in Fastq files?

answered Aug 19, 2017 at 6:34

4 votes

How to extract / convert gff3 CDS sequences to multifasta

answered Aug 21, 2017 at 11:23

4 votes

Accepted

How to find novel transcripts using GFFcompare?

answered Jul 17, 2019 at 12:13

3 votes

Produce a single sequential FASTA sequence out of BAM

answered Jul 5, 2019 at 7:41

3 votes

Accepted

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

answered Dec 8, 2021 at 16:25

2 votes

Accepted

PASA pipeline: compare experimental transcripts to the reference annotation

answered Jul 6, 2017 at 7:35

2 votes

At what processing step should library strandedness type be taken into account?

answered Jul 18, 2017 at 15:07

2 votes

Accepted

gffread: GFaSeqGet errors on coordinate overhang

answered Feb 27, 2018 at 14:55

2 votes

How to get Nanopore MinION fast5 from SRA

answered Nov 27, 2017 at 15:11

2 votes

What is a standard approach to binarize microarray gene expression data?

answered Apr 10, 2018 at 6:20

1 vote

Accepted

Is it possible to find out the PacBio chemistry from the PacBio Sequel BAM's header?

answered Feb 9, 2018 at 16:15

1 vote

Exon-exon junctions: compare experimental transcripts to reference annotation

answered Feb 12, 2018 at 13:39

1 vote

Introduce errors in reference transcripts according to external dataset error model

answered Aug 24, 2017 at 13:36

1 vote

Is it wise to use RepeatMasker on prokaryotes?

answered Aug 29, 2017 at 22:20

1 vote

Accepted

Mark BWA-SW split alignments in output for long reads

answered Nov 6, 2017 at 11:02

1 vote

full visualisation of draft genomes alignment

answered Nov 26, 2018 at 7:26

Stack Exchange Network

24 Answers

Extracting expression data from GSE dataset downloaded from GEO

What format is this? Pretty sure it's not a BED file

Cufflinks Error: sort order of reads in BAMs must be the same

full visualisation of draft genomes alignment

How to measure the total size of a fastq file in base pairs?

Converting a BAM file into VCF

Salmon tximport

visualisation of genome alignment

Is there a way to quickly verify the presence of some SNPs in Fastq files?

How to extract / convert gff3 CDS sequences to multifasta

How to find novel transcripts using GFFcompare?

Produce a single sequential FASTA sequence out of BAM

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

PASA pipeline: compare experimental transcripts to the reference annotation

At what processing step should library strandedness type be taken into account?

gffread: GFaSeqGet errors on coordinate overhang

How to get Nanopore MinION fast5 from SRA

What is a standard approach to binarize microarray gene expression data?

Is it possible to find out the PacBio chemistry from the PacBio Sequel BAM's header?

Exon-exon junctions: compare experimental transcripts to reference annotation

Introduce errors in reference transcripts according to external dataset error model

Is it wise to use RepeatMasker on prokaryotes?

Mark BWA-SW split alignments in output for long reads

full visualisation of draft genomes alignment