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Old 11-18-2016, 02:59 AM   #1
JOM...
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Location: SPAIN

Join Date: Nov 2016
Posts: 1
Default Too much "no feature" counts??

Hello,
Iím having some issues analysing RNASeq data on Chipster. I have single-end rna samples (brain) sequenced on a illumina NextSeq platform from rattus norvergicus.
When i run the TopHat (Rattus6.0.83/fr-firststrand/20 hits allowed per read/Ö) i obtain:

Reads:
Input : 29084606
Mapped : 27577865 (94.8% of input)
of these: 1284892 ( 4.7%) have multiple alignments (17957 have>20)
94.8% overall read mapping rate.

When running the HTSeq (Rattus6.0.83/"reverse"/no paired end/chromosome names in the BAM "1"/ union / exon / gene_id) for counting the reads per gene i found a lot of no_feature reads.

__no_feature 7413760
__ambiguous 111934
__too_low_aQual 0
__not_aligned 0
__alignment_not_unique 4203664

Is it normal?

Then in the differential expression using the DESeq2 i get extremely few or even no significant padj values. Only get 12 signicant padj values even compairing MALES VH and FEMALES VH which seems quite shocking to us.
Iím i doing something wrong?
Thank you very much in advance for the help.
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rnaseq alignment, rnaseq analysis, rnaseq deseq padj, rnaseq htseq

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