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Old 06-27-2013, 11:17 AM   #1
muthu545
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Location: san antonio

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Posts: 32
Default HTSeq to DESeq

Hi all,

HTSeq's count file output contains # of reads for
no_feature
ambiguous
too_low_aQual
not_aligned
alignment_not_unique

I used to delete them from my gene matrix before inputting that
to DESeq's newCountDataSet.

Is it okay to do it this way or have these 5 feature_id's in the data
matrix when performing DE analysis using DESeq
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Old 06-28-2013, 04:11 AM   #2
Simon Anders
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You are correct, you should delete them.
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Old 06-28-2013, 06:34 AM   #3
muthu545
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Thank you, Simon.
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Old 01-29-2014, 08:21 AM   #4
tschauer
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Hi Simon,

The DESeq2 vignette (HTSeg input) confused me about this. The "_lowaqual" is still in there. See

ddsHTSeq
class: DESeqDataSet
dim: 70467 7
exptData(0):
assays(1): counts
rownames(70467): FBgn0000003:001 FBgn0000008:001 ... _lowaqual
_notaligned
rowData metadata column names(0):
colnames(7): treated1fb.txt treated2fb.txt ... untreated3fb.txt
untreated4fb.txt
colData names(1): condition
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