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5
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1
answer
115
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1
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how to get correlation between the counts over each gene at the same timepoint (two replicates)
htseq correlation rna-seq replication written 4 days ago by Lila M • 410 • updated 4 days ago by Nicolas Rosewick ♦ 7.2k
1
vote
1
answer
232
views
1
answer
htseq-count SAM Processing error "can't decode byte 0xa7"
htseq rna-seq written 6 weeks ago by Glubbdrubb • 0
2
votes
1
answer
204
views
1
answer
What's the difference of FPKM generated by htseq and stringtie?
htseq fpkm stringtie written 6 weeks ago by hxlei613 • 80 • updated 6 weeks ago by Devon Ryan ♦ 87k
6
votes
2
answers
154
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5 follow
2
answers
counting number of genes located on positive or negative strands
gff3 htseq written 11 weeks ago by arsilan324 • 60 • updated 11 weeks ago by mike-zx • 110
9
votes
2
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477
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7 follow
2
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How to input data for DESeq2 from individual HTSeq count?
htseq deseq2 deseq rna-seq written 3 months ago by sudu87 • 10 • updated 3 months ago by poojasethiya • 80
0
votes
0
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148
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0
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Generating read counts for my microRNA reads for a non model invertebrate
htseq small rna read count microrna written 3 months ago by karthic • 100
0
votes
1
answer
162
views
1
answer
HTseq-counts not counting correctly?
htseq drosophila rna-seq written 3 months ago by vm.higareda • 20
0
votes
0
answers
251
views
0
answers
RNA-seq High Variation Between and Within Groups
htseq tophat2 rna-seq written 4 months ago by jacobsen.jeremy • 40 • updated 4 months ago by h.mon ♦ 22k
0
votes
1
answer
397
views
1
answer
Should I include multi-mapped reads for analysis that does not require significant differential expression of genes?
htseq heatmap multi-mapped clustering rna-seq written 7 months ago by k.woolf • 0 • updated 5 months ago by Vincent Laufer • 1.0k
10
votes
1
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431
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1
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calculating the fpkm from htseq counts
htseq R fpkm rna-seq written 7 months ago by shenwei1376 • 0 • updated 7 months ago by Charles Warden ♦ 5.9k
1
vote
1
answer
919
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1
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htseq-count: error when reading beginning of SAM/BAM file.
htseq htseq-count rna-seq written 8 months ago by cgias • 0 • updated 8 months ago by h.mon ♦ 22k
2
votes
2
answers
243
views
2
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How reads are considered as mapped using samtools idxstats?
htseq idxstats samtools written 8 months ago by Vijay Lakhujani ♦ 3.5k • updated 8 months ago by Pierre Lindenbaum ♦ 116k
0
votes
0
answers
290
views
0
answers
What to do with unpaired reads post-trimming?
de-novo htseq trimming metagenomic mapping written 8 months ago by willnotburn • 40
0
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0
answers
341
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0
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strand-specific metagene analysis
htseq strand-specific rna-seq metagene written 9 months ago by yuabrahamliu • 40
3
votes
1
answer
496
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1
answer
HTSeq not finding any features in mapped rnaseq file
htseq rna-seq written 10 months ago by AGC • 0 • updated 10 months ago by h.mon ♦ 22k
0
votes
0
answers
284
views
0
answers
HTSeq-count ambiguous results - all transcripts vs. single transcript
htseq gene rna-seq written 10 months ago by oriolebaltimore • 60
7
votes
1
answer
870
views
1
answer
Error in extracting Counts from the bam file using htseq-count
htseq bam counts rna-seq written 11 months ago by Biologist • 120 • updated 11 months ago by h.mon ♦ 22k
0
votes
0
answers
291
views
0
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Filter HT-Seq output for gene subclasses
htseq transcription factor rna-seq written 11 months ago by rbronste • 230
0
votes
0
answers
297
views
0
answers
Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
htseq deeptools pysam written 11 months ago by ZheFrench • 180
0
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0
answers
481
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0
answers
Counting reads in CDS - but skipping few first/last codons
htseq rna-seq written 12 months ago by PocketChange • 0
6
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0
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749
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0
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What GTF file should I use in htseq?
htseq hisat rna-seq polyester written 13 months ago by statfa • 410 • updated 13 months ago by genomax ♦ 60k
3
votes
0
answers
565
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0
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HTSeq special counters occur at top and bottom of output file
htseq written 13 months ago by mccormack • 20
10
votes
1
answer
992
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5 follow
1
answer
Copy number variation using HTSeq/DESeq2
htseq copy number deseq written 13 months ago by ThePresident • 100 • updated 13 months ago by WouterDeCoster ♦ 36k
2
votes
1
answer
1.1k
views
1
answer
How to specify the sort based on name in samtools sort?
htseq bam samtools rna-seq sort written 13 months ago by anc.informatics • 0 • updated 13 months ago by finswimmer ♦ 8.9k
4
votes
1
answer
1.4k
views
1
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Why Warning: reads with missing mate encountered is occured in HTSeq?
htseq alignment sam rna-seq written 14 months ago by anc.informatics • 0 • updated 14 months ago by Martombo • 2.4k
4
votes
1
answer
1.8k
views
1
answer
htseq-count error Feature does not contain a 'gene_id' attribute
htseq gff read count rna-seq written 14 months ago by madzayasodara • 10 • updated 14 months ago by WouterDeCoster ♦ 36k
1
vote
1
answer
624
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1
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HTSeq funny output
htseq quantification rna-seq written 14 months ago by --panda-- • 30
1
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0
answers
751
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0
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warning message after HTSeq
software error htseq rna-seq written 15 months ago by BioDH • 0
0
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0
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644
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0
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GAPDH missing from htseq-counts file
htseq gapdh nonunique written 15 months ago by melia_g • 0
0
votes
0
answers
362
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0
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htseq ignores contiges with zero reads
htseq written 15 months ago by statfa • 410
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