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htseqgenie
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HTSeq command option for single-end reads
HTSeqGenie
20 months ago
Maryam.sed1400
• 0
2
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1
reply
1.2k
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Source of ribosomal RNA sequences to build rrna_genome index for the HTSeqGenie package
HTSeqGenie
updated 7.7 years ago by
Jens Reeder
▴ 40 • written 7.7 years ago by
Thomas Sandmann
▴ 90
0
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0
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845
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HISAT2 and HTSEQ command
HTSeqGenie
19 months ago
Maryam.sed1400
• 0
1
vote
1
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455
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HTSeqGenie run error
HTSeqGenie
14 months ago
zh9118
• 0
0
votes
1
reply
303
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HTSeqGenie runs very slow
HTSeqGenie
7 months ago • updated 6 months ago
zh9118
• 0
0
votes
1
reply
134
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
zh9118
• 0
6 results • Page
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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