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5
votes
2
answers
751
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2
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Non-ascii characters in bam file cause htseq-count error
htseq-count star rna-seq written 12 days ago by loui_ • 0 • updated 12 days ago by swbarnes2 ♦ 6.7k
6
votes
2
answers
230
views
5 follow
2
answers
is 0-based start and 1-based end of bed format not compatible with htseq-count?
index-error 0-based start htseq-count bed to gtf written 4 weeks ago by Zee_S • 40 • updated 4 weeks ago by michael.ante • 3.5k
1
vote
0
answers
91
views
0
answers
HT-seq-count default parameter to "score"secondary alignments contradicts its documentation that it ignores multi mappers by default. Not clear!
secondary alignment htseq-count multimapping read written 5 weeks ago by Zee_S • 40
2
votes
0
answers
139
views
0
answers
Can we make a counting program using GFF3 reference files?
rnaseq htseq-count featurecounts written 9 weeks ago by ino • 0
6
votes
2
answers
264
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2
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Question about exon/intron counting in RNA-seq dataset analysis
htseq-count featurecounts rna-seq written 5 months ago by nanoide • 30 • updated 5 months ago by swbarnes2 ♦ 6.7k
0
votes
1
answer
420
views
1
answer
Ambiguous reads in htseq-count
htseq-count rna-seq written 6 months ago by kousi31 • 0
2
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1
answer
210
views
1
answer
how to get gff file bos tau8 from ucsc to import in usegalaxy
gff ucsc htseq-count usegalaxy written 6 months ago by Kian • 40
0
votes
1
answer
578
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5 follow
1
answer
FASTQ alignment result is really bad
htseq-count salmon rna-seq written 10 months ago by bharata1803 • 430 • updated 10 months ago by h.mon ♦ 27k
4
votes
1
answer
629
views
1
answer
STAR quantMode geneCounts: weird outcomes
htseq-count star rna-seq written 12 months ago by davide.chiarugi • 20
0
votes
0
answers
426
views
0
answers
Normalization of read counts from HTSeq by library size
R htseq-count deseq2 ngs rna-seq written 12 months ago by Susmita Mandal • 50
5
votes
1
answer
477
views
1
answer
Ovation RNA-seq system, bionfomatic alignment and htseq-count
htseq-count rna-seq hisat2 written 12 months ago by nanoide • 30 • updated 12 months ago by caggtaagtat • 800
0
votes
1
answer
1.3k
views
1
answer
Malformed SAM line error with HTSeq
htseq-count written 3.7 years ago by Kssr • 110 • updated 13 months ago by RamRS ♦ 24k
2
votes
0
answers
907
views
0
answers
featurecounts more fragments than input read pairs
htseq-count featurecounts pair-end rna-seq written 14 months ago by ewre • 220 • updated 13 months ago by Biostar ♦♦ 20
1
vote
0
answers
612
views
0
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Htseq: High number of no_feature
htseq-count rna-seq written 13 months ago by nadja.g • 0 • updated 13 months ago by genomax ♦ 73k
5
votes
2
answers
649
views
2
answers
Salmon quantification vs HTSeq count quantification
htseq-count salmon written 13 months ago by vincentpailler • 100 • updated 13 months ago by h.mon ♦ 27k
0
votes
0
answers
662
views
0
answers
Preprocessing for DESeq2 - create metadata table
htseq-count deseq2 rna-seq written 14 months ago by alexadeanfitz • 10 • updated 14 months ago by h.mon ♦ 27k
2
votes
1
answer
849
views
1
answer
htseq-count error utf-8 codec can't decode
htseq-count rna-seq written 14 months ago by alexadeanfitz • 10
3
votes
1
answer
552
views
5 follow
1
answer
Using HTseq-count for Pseudomonas Aeruginosa data
htseq-count rna-seq written 14 months ago by jspainhour3 • 10
4
votes
1
answer
1.1k
views
1
answer
Difference between HTSeq-count & Salmon quant results
htseq-count salmon rna-seq written 14 months ago by vincentpailler • 100 • updated 14 months ago by genomax ♦ 73k
4
votes
0
answers
1.1k
views
5 follow
0
answers
HTSeq-count in RNA-Seq
htseq-count rna-seq written 15 months ago by mlemusfuentes • 10
2
votes
1
answer
525
views
1
answer
reasons for htseq-count with zero features
htseq-count rna-seq written 16 months ago by shenwei1376 • 0 • updated 16 months ago by genomax ♦ 73k
11
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4
answers
3.1k
views
4
answers
Run htseq-count with multiple sam files?
htseq-count rna-seq written 3.3 years ago by lynne.m.a.harris • 10 • updated 16 months ago by kristoffer.vittingseerup • 2.4k
4
votes
1
answer
867
views
1
answer
HTSeq-count [Python] is not properly counting reads like Genomic Alignments [R] ?
htseq-count rna-seq genomicalignments written 16 months ago by badredda • 110
0
votes
0
answers
423
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0
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Inaccurate read counts when genome/annotation contains alternate loci
htseq-count star rna-seq alternative loci written 17 months ago by viktorfeketa • 20
12
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2
answers
5.9k
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2
answers
how to use a bed file with htseq-count
htseq-count rna-seq written 5.4 years ago by Ann • 2.2k • updated 17 months ago by Biostar ♦♦ 20
4
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0
answers
654
views
0
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Enough counts for RNA-Seq differential expression analysis
htseq-count rna-seq written 17 months ago by skhan • 10
3
votes
1
answer
834
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1
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Which htseq-count mode to use for handling overlaps during RNA-Seq quantitation
htseq-count rna-seq written 17 months ago by skhan • 10 • updated 17 months ago by lieven.sterck ♦ 6.0k
1
vote
1
answer
1.8k
views
1
answer
htseq-count: error when reading beginning of SAM/BAM file.
htseq htseq-count rna-seq written 17 months ago by cgias • 0 • updated 17 months ago by h.mon ♦ 27k
3
votes
0
answers
977
views
5 follow
0
answers
Htseq-count: discrepancy between raw count value and viewable value of reads on BAM with IGV
htseq-count rna-seq written 21 months ago by sophie.ehresmann • 10 • updated 19 months ago by Biostar ♦♦ 20
0
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1
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2.2k
views
1
answer
featureCounts/HTSeq-count problem with different annotation files
htseq-count featurecounts rna-seq written 4.0 years ago by monteiro.s.rita • 0 • updated 19 months ago by Biostar ♦♦ 20
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