User: 2822462298

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282246229810
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Posts by 2822462298

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Several questions about miRDeep2
... Hi all, I am currently using miRDeep2 to identify miRNAs in a non-model organism (a butterfly). After running mapper.pl to map the small RNA reads to the genome, I used miRDeep2.pl to predict novel miRNAs of the species. Here are some of my questions: 1. I have 8 samples with 2 conditions (4 replic ...
mirna srna-seq mirdeep2 rna-seq written 23 hours ago by 282246229810
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Comment: C: How to interpret the differences of read counts using htseq and feature counts?
... Thanks Michael, I tried including -Q 10 in featurecounts and got "Unassigned_MappingQuality 27689", and the counts remain almost unchanged. Apparently, htseq somehow filtered out more reads other than quality filter. ...
written 4 days ago by 282246229810
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Comment: C: How to interpret the differences of read counts using htseq and feature counts?
... Thanks Michael, I tried including the -B option but the counts only reduced a little, they are still much higher than htseq. ...
written 4 days ago by 282246229810
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Comment: C: How to interpret the differences of read counts using htseq and feature counts?
... Hi genomax, I understand and I really appreciate all the suggestions provided. I apologize if I may sound a little bit impatient. ...
written 4 days ago by 282246229810
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Comment: A: How to interpret the differences of read counts using htseq and feature counts?
... Any ideas guys? :((( ...
written 4 days ago by 282246229810
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Comment: C: How to interpret the differences of read counts using htseq and feature counts?
... Just checked for all my unsorted, name-sorted, and position-sorted files, it shows @HD VN:1.0 SO:unsorted @HD VN:1.0 SO:queryname @HD VN:1.0 SO:coordinate respectively. I guess there is nothing wrong with the sorting. ...
written 4 days ago by 282246229810 • updated 4 days ago by genomax76k
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Comment: C: How to interpret the differences of read counts using htseq and feature counts?
... I have read that post but I still did not find an explanation for the big gap between the two programs, I know it has something to do with my basic setting but I really don't know what's wrong with it since I did read the manuals very carefully... ...
written 5 days ago by 282246229810
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How to interpret the differences of read counts using htseq and feature counts?
... Hi all, To make it simple. I tried both htseq and featurecounts to generate read counts for differential expressed gene analyisis using deseq2. Here are example outputs for one of my samples: 1. Htseq (input bam file sorted by name using sortmeRNA) code: `htseq-count -f bam -i Name ${i}_final_by ...
htseq next-gen featurecounts rna-seq written 5 days ago by 282246229810 • updated 4 days ago by michael.ante3.6k
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Comment: C: optimise htseq count performance by choosing proper samtools sort options
... Thanks! Actually I have tried all name, postion, and unsorted bam files for featurecounts. The outputs were pretty much the same with minor differences. ...
written 6 days ago by 282246229810
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Comment: C: optimise htseq count performance by choosing proper samtools sort options
... Thanks! In that case I do not need to sort the bam file using samtools right? ...
written 6 days ago by 282246229810

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