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<prev • 241 results • page 1 of 9 • next >
0
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answers
70
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How splice-aware aligner (RNA-Seq) deal with long gap (intron) penalty
hisat tophat alignment star rna-seq written 20 hours ago by CY • 370
2
votes
2
answers
150
views
2
answers
How I deal with raw read counts of RNA-seq
deseq2 star rna-seq written 10 days ago by Angel • 3.5k • updated 10 days ago by swbarnes2 ♦ 6.5k
4
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0
answers
4.1k
views
0
answers
STAR - genome indexes generation, genome file not created
star rna-seq written 2.8 years ago by lu.ne • 70 • updated 17 days ago by Biostar ♦♦ 20
16
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4
answers
218
views
7 follow
4
answers
How I deal with different lanes in RNA-seq alignment
alignment star rna-seq written 17 days ago by Angel • 3.5k • updated 17 days ago by leaodel • 100
2
votes
2
answers
187
views
2
answers
featureCounts error with 150bp Paired end RNA seq data
ngs featurecounts paired-end rna-seq star written 6 weeks ago by ankuresearch • 10 • updated 23 days ago by swbarnes2 ♦ 6.5k
0
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0
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120
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0
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trimming A tails: clip3pAdapterSeq in star vs cutadapt
star rna-seq written 25 days ago by wiscoyogi • 0
1
vote
1
answer
101
views
1
answer
When (not to) pre-build a STAR index
genome-index star written 5 weeks ago by jhanks1981 • 0 • updated 5 weeks ago by Thibault D. • 650
3
votes
1
answer
148
views
1
answer
BAM File size increased after extracting unique reads
alignment samtools star bam uniuque mapping written 5 weeks ago by ilovesuperheroes1993 • 0 • updated 5 weeks ago by michael.ante • 3.4k
1
vote
1
answer
179
views
1
answer
How to access STAR index loaded into shared memory
alignment star rna-seq written 12 weeks ago by paulranum11 • 40 • updated 9 weeks ago by Artem Kiselev • 20
5
votes
2
answers
257
views
5 follow
2
answers
>99% unmapped reads
star rna-seq written 10 weeks ago by RPuni • 0 • updated 10 weeks ago by swbarnes2 ♦ 6.5k
11
votes
4
answers
462
views
6 follow
4
answers
Dealing with 1000's of demultiplexed fastq files
zumis star umi-tools written 5 months ago by volvicpellegrino • 0 • updated 12 weeks ago by Lior Pachter • 370
13
votes
2
answers
232
views
2
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What are the best set of options to use while aligning using STAR?
ngs alignment star rna-seq written 3 months ago by gprashant17 • 60 • updated 3 months ago by Charles Warden ♦ 7.2k
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1
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1.8k
views
1
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How Splice Junction database(SJ.out.tab) is generated from GTF(ENSEMBL) and Reference Genome (GRCh38) using STAR Aligner during Genome indexing
gtf hisat star splice junction assembly written 2.1 years ago by inambioinfo • 100 • updated 3 months ago by yywang113 • 10
1
vote
1
answer
254
views
1
answer
STAR+HTSeq gene counts vs STAR+RSEM genes and how to combine isoforms to get the gene counts?
htseq gene star isoform rsem written 3 months ago by jennygenome • 0 • updated 3 months ago by swbarnes2 ♦ 6.5k
3
votes
2
answers
387
views
2
answers
STAR mapping pipeline with 2-pass for multiple samples?
2-pass multiple samples expression star rna-seq written 3 months ago by Rajesh Detroja • 60
5
votes
1
answer
263
views
1
answer
What is Canonical/Non-canonical splicing?
ngs alignment star rna-seq splicing written 3 months ago by gprashant17 • 60 • updated 3 months ago by Jean-Karim Heriche ♦ 20k
2
votes
2
answers
245
views
2
answers
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
alignment featurecounts star rna-seq written 3 months ago by garbuzov • 10
9
votes
3
answers
196
views
3
answers
Divergent number of replicates between FastQC and samtools
samtools star fastqc written 3 months ago by user31888 • 70 • updated 3 months ago by i.sudbery ♦ 5.3k
3
votes
1
answer
170
views
1
answer
Fail to delete temporary folder
rsem star shell written 3 months ago by prabin.dm • 160
0
votes
0
answers
136
views
0
answers
How bad is it if chromosome patches are included in STAR alignmnet, and is it possible to fix this?
alignment star written 4 months ago by chicheheda • 0 • updated 4 months ago by RamRS ♦ 24k
1
vote
0
answers
205
views
0
answers
Which genome files to use for STAR?
genome alignment star written 4 months ago by Nico80 • 0
0
votes
0
answers
166
views
0
answers
Ensembl assembly choice for RNA-Seq reference mapping
ensembl alignment star rna-seq assembly written 4 months ago by eoin • 30 • updated 4 months ago by genomax ♦ 71k
0
votes
1
answer
157
views
1
answer
Different % alignment in Log Final & sum of ReadsPerGene
star written 4 months ago by andrebolerbarros • 0 • updated 4 months ago by swbarnes2 ♦ 6.5k
7
votes
1
answer
412
views
1
answer
Counting No. of Reads per gene from RNA-Seq with STAR
star rna-seq written 4 months ago by skevalkumar • 0 • updated 4 months ago by h.mon ♦ 27k
0
votes
1
answer
235
views
1
answer
How should i determine outFilterMultimapNmax in rna seq analysis, P.s im working on pseudogenes.
pseudogenes star rna-seq written 5 months ago by sabaghianamir70 • 10 • updated 5 months ago by h.mon ♦ 27k
2
votes
1
answer
442
views
5 follow
1
answer
Infer experiment - Failed to determine strandin paired end stranded RNA-seq
hisat2 paired end star rna-seq stranded written 9 months ago by GiusiG • 0 • updated 5 months ago by zoegward • 60
3
votes
1
answer
263
views
1
answer
Chunks erros with STAR aligner
star rna-seq written 5 months ago by Morris_Chair • 120
12
votes
3
answers
642
views
6 follow
3
answers
Running STAR aligner with paired-end and single-end reads simultaneously
paired-end star single-end rna-seq written 6 months ago by nanoide • 30
6
votes
1
answer
473
views
1
answer
Problem with generating BAM files with STAR
star rna-seq written 5 months ago by gokberk • 60
6
votes
1
answer
397
views
1
answer
How to run STAR for multiple fastq files without overwriting?
star written 5 months ago by gokberk • 60
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