User: xiaofeiwang198266

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Posts by xiaofeiwang198266

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Comment: C: DiffBind: reading in peaksets generated by Homer2
... Hi Gord, I think it should be $3-1 for the start position.  My understanding is that BED format is 0-based for the second column (chromStart), while it is 1-based for the peak txt file from HOMER. I double checked the script of "pos2bed.pl", which is "my $start = $line[2]-1;" to get start position. ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: DiffBind: reading in peaksets generated by Homer2
... The reason for the fifth column are all set to 1 is that I think there is a bug in the Perl script of pos2bed.pl? Not matter you use "-5" option or not (-5 : Set 5th column to the value 1 instead of value in 6th column of pos file), the fifth column will be 1 always. ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: ChIPseeker question: provide custom csAnno to plots
... Yes, it totally makes sense. But could you tell me how the distance to TSS is calculated (I will look up this too)? Because I see they are much different between homer and chipseeker, not only the number but also the sign (+/-). Please refer to the example at the bottom, the distance is 1312 VS -894 ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: ChIPseeker question: provide custom csAnno to plots
... yes, I sent you the related files to your Gmail. Please let me know, if you can't open it. Thanks a lot! BEST, Xiaofei ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: ChIPseeker question: provide custom csAnno to plots
... Also, I compared the annotation between ChIPseeker with another tool. The first few lines results are listed above (hope you can get the meaning for each column because of bad format. I don't know how to upload an image from my laptop). The Nearest.PromoterID are same between them. But the distance ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: ChIPseeker question: provide custom csAnno to plots
... Annotation Distance.to.TSS Nearest.PromoterID geneId_chipseeker annotation_chipseeker distanceToTSS_chipseeker exon (transcript:Sb08g023250.1, exon 1 of 1) 1312 transcript:Sb08g023250.1 Sb08g023250 Promoter (<=1kb) 0 exon (transcript:Sb08g0 ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: ChIPseeker question: provide custom csAnno to plots
... I think I should find a way to do this. I see ChIPseeker can accept a GRanges object. So, what I did is that I made a GRanges object from a data frame by makeGRangesFromDataFrame. Then, I used this as the input of ChIPseeker to do plots. Also, I used makeTxDbFromGFF to create TxDb from a GFF3 file. ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: ChIPseeker question: provide custom csAnno to plots
... Hi Guangchuang, is there any way I can convert a TXT file (external annotated peak file) to a csAnno object? In other words, could ChIPseeker take external annotated peak file to do plots? Thanks a lot! BEST, Xiaofei ...
written 7 months ago by xiaofeiwang1982660
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Comment: C: DESeq2 negative tab counts
...   I did send an email and cross my fingers to get response from them. Here is the command that I used for HOMER, it is very easy and just one-line command. getDifferentialPeaksReplicates.pl -t IP1_tagDir IP2_tagDir IP3_tagDir -i Inp1_tagDir/ Inp2_tagDir/ bInp3_tagDir/ -genome AGPv3 -gsize 2.2e9 & ...
written 13 months ago by xiaofeiwang1982660
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DESeq2 negative tag counts
... Dear there, Is it expected to get negative tag count by using DESeq2? I am using HOMER (getDifferentialPeaksReplicates.pl http://homer.ucsd.edu/homer/ngs/peaksReplicates.html) for my analysis, which uses R/Bioconductor and DESeq2 (by default) to perform the differential enrichment calculations. Wh ...
deseq2 written 13 months ago by xiaofeiwang1982660

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