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Showing :
questions
6
votes
14
replies
3.1k
views
Alignment with STAR produces unique bam files, but identical output from bedtools multicov
bedtools
STAR
samtools
updated 4.3 years ago by
Biostar
20 • written 8.0 years ago by
dec986
▴ 370
1
vote
4
replies
1.1k
views
Break_blocks conversion of gvcf -> vcf
VCF
updated 4.3 years ago by
ATpoint
82k • written 4.3 years ago by
dec986
▴ 370
1
vote
1
reply
602
views
creating specific bed file from VCF
vcf
vcf2bed
4.4 years ago by
dec986
▴ 370
11
votes
6
replies
2.1k
views
Cannot identify software used to make image
DMR
updated 5.2 years ago by
bernatgel
★ 3.4k • written 5.2 years ago by
dec986
▴ 370
2
votes
6
replies
1.8k
views
Diploid calls on chrY?
genome
vcf
updated 5.3 years ago by
finswimmer
16k • written 5.3 years ago by
dec986
▴ 370
4
votes
6
replies
2.8k
views
samtools sort doesn't finish sorting bam file, just hangs for hours
samtools
5.5 years ago by
dec986
▴ 370
0
votes
5
replies
2.7k
views
Zero Counts for many genes in 1 replicate, why?
cufflinks
RNA-Seq
updated 17 months ago by
Ram
43k • written 8.9 years ago by
dec986
▴ 370
3
votes
2
replies
1.3k
views
Measure Sequencing Depth in aligned BAM file
RNA-Seq
updated 5.7 years ago by
Biostar
20 • written 5.8 years ago by
dec986
▴ 370
1
vote
5
replies
3.5k
views
Differential Expression with Ballgown
RNA-Seq
R
updated 5.7 years ago by
Biostar
20 • written 5.8 years ago by
dec986
▴ 370
1
vote
10
replies
5.5k
views
how to get counts/TPM/etc. from stringtie?
RNA-Seq
updated 5.8 years ago by
sanchi.andrea
• 0 • written 5.8 years ago by
dec986
▴ 370
2
votes
3
replies
2.2k
views
R: Ballgown load fails
RNA-Seq
R
software error
5.8 years ago by
dec986
▴ 370
2
votes
1
reply
1.5k
views
samtools stats typical ranges and explicit definitions
samtools
RNA-Seq
5.8 years ago by
dec986
▴ 370
4
votes
1
reply
3.4k
views
Meaning of Decimal points in ENST notation
rna-seq
updated 5.9 years ago by
goodez
▴ 640 • written 5.9 years ago by
dec986
▴ 370
0
votes
0
replies
1.8k
views
MSigDB gene set enrichment analysis
gene ontology
gsea
6.1 years ago by
dec986
▴ 370
0
votes
0
replies
1.6k
views
Choice of Gene Length in TPM Calculations
RNA-Seq
tpm
6.2 years ago by
dec986
▴ 370
0
votes
2
replies
1.2k
views
Creating genome alignment
STAR
RNA-Seq
updated 6.2 years ago by
lshepard
▴ 470 • written 6.2 years ago by
dec986
▴ 370
8
votes
8
replies
4.3k
views
STAR Alignment Score reduced after trimming
STAR
RNA-Seq
updated 6.2 years ago by
Devon Ryan
104k • written 6.2 years ago by
dec986
▴ 370
8
votes
1
reply
5.3k
views
STAR => featureCounts pipeline
RNA-Seq
updated 6.2 years ago by
h.mon
35k • written 6.2 years ago by
dec986
▴ 370
3
votes
1
reply
1.4k
views
Trimmomatic destroys right-hand paired-end sequences, how to avoid?
trimmomatic
qc
updated 6.3 years ago by
Martombo
★ 3.1k • written 6.3 years ago by
dec986
▴ 370
5
votes
3
replies
1.4k
views
Cannot match machine name with Machine Type
RNA-Seq
fastq
trimmomatic
qc
updated 6.3 years ago by
Devon Ryan
104k • written 6.3 years ago by
dec986
▴ 370
6
votes
11
replies
6.3k
views
stringtie cannot recognize Gencode GTF
RNA-Seq
stringtie
gencode
updated 6.3 years ago by
geo.pertea
▴ 130 • written 6.3 years ago by
dec986
▴ 370
3
votes
2
replies
3.0k
views
featureCounts not recognizing paired-end alignment file.. why?
featurecounts
RNA-Seq
6.4 years ago by
dec986
▴ 370
4
votes
1
reply
2.8k
views
Cuffcompare output: thousands of novel transcripts
cuffcompare
RNA-Seq
updated 6.4 years ago by
Kevin Blighe
87k • written 6.4 years ago by
dec986
▴ 370
0
votes
2
replies
2.9k
views
Tophat with mm10 gencode
RNA-Seq
alignment
updated 20 months ago by
Ram
43k • written 8.6 years ago by
dec986
▴ 370
14
votes
5
replies
6.9k
views
How to repair *all* problems identified by FastQC?
RNA-Seq
FastQC
updated 6.4 years ago by
Ian
6.0k • written 6.4 years ago by
dec986
▴ 370
0
votes
2
replies
1.3k
views
how to fix Kmer count from FastQC?
fastQC
RNA-Seq
updated 6.4 years ago by
realnewbie
▴ 30 • written 6.4 years ago by
dec986
▴ 370
2
votes
4
replies
1.7k
views
Fastq-Dump Crashes, how to prevent besides continually restarting?
SRA
fastq-dump
NCBI
6.4 years ago by
dec986
▴ 370
7
votes
6
replies
1.7k
views
Solutions to FastQC diagnosis of Micro-Satellites
fastqc
RNA-Seq
6.4 years ago by
dec986
▴ 370
0
votes
0
replies
1.2k
views
BiSeq manual giving incompatible objects
R
BiSeq
6.5 years ago by
dec986
▴ 370
5
votes
9
replies
5.8k
views
'BiocParallel' did not register default BiocParallelParams
software error
R
6.5 years ago by
dec986
▴ 370
4
votes
3
replies
1.1k
views
Searching Gene Ontology for Known Organs
gene ontology
7.1 years ago by
dec986
▴ 370
10
votes
4
replies
15k
views
Long Read Length, yet STAR says many reads too short
STAR
RNA-Seq
single-cell
alignment
updated 7.1 years ago by
datascientist28
▴ 560 • written 7.1 years ago by
dec986
▴ 370
0
votes
3
replies
2.6k
views
Picard MergeBamAlignment failure
picard
drop-seq
7.2 years ago by
dec986
▴ 370
0
votes
2
replies
3.0k
views
How to get correct options for Picard's AddOrReplaceReadGroups?
picard
7.3 years ago by
dec986
▴ 370
1
vote
3
replies
2.3k
views
Quantification of Maps to rRNA and mtDNA
rRNA
RNA-Seq
alignment
star
mtRNA
updated 7.4 years ago by
Devon Ryan
104k • written 7.4 years ago by
dec986
▴ 370
4
votes
9
replies
3.6k
views
How to plot "normalized read density" vs "insert size"
RNA-Seq
updated 7.5 years ago by
ATpoint
82k • written 7.5 years ago by
dec986
▴ 370
6
votes
4
replies
6.0k
views
STAR aligner fails to produce unmapped file
STAR
updated 7.5 years ago by
WouterDeCoster
47k • written 7.5 years ago by
dec986
▴ 370
5
votes
2
replies
12k
views
edgeR: no residual df: Cannot estimate dispersion
edgeR
updated 7.6 years ago by
Devon Ryan
104k • written 7.6 years ago by
dec986
▴ 370
0
votes
7
replies
3.7k
views
Installation of Bcl2Fastq Fails
bcl2fastq
basespace
software error
illumina
7.9 years ago by
dec986
▴ 370
6
votes
3
replies
1.7k
views
Where Can I download Less Common Genomes?
fasta
RNA-Seq
genome
updated 13 months ago by
Ram
43k • written 7.9 years ago by
dec986
▴ 370
1
vote
5
replies
5.0k
views
FeatureCounts Not Reading GTF File Correctly
featureCounts
RNA-Seq
7.9 years ago by
dec986
▴ 370
1
vote
5
replies
4.5k
views
DESeq2 comparison failure
RNA-Seq
R
updated 19 months ago by
Ram
43k • written 8.7 years ago by
dec986
▴ 370
1
vote
2
replies
3.1k
views
Conversion between .bedGraph or .bw to 7-column format
format-conversion
DNA-methylation
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
dec986
▴ 370
93 results • Page
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