User: nanoide

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nanoide30
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3 days ago
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1 year, 11 months ago
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Posts by nanoide

<prev • 41 results • page 1 of 5 • next >
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ATACseqQC factorFootprints function
... Hi, I have a question about the plot coming frm the factorFootprints, as in the ATACseqQC vignette: https://bioconductor.org/packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html#plot-footprints What are the red dashed horizontal lines? Some kind of average? I tried to look for the ans ...
footprint atac-seq atacseqqc written 4 weeks ago by nanoide30
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Help filling the configuration file for the masurca assembler
... Hi, So I would like to try the MaSuRCA assembler using Illumina short paired-end reads and pacbio long reads. 1.- I saw in the configuration file that one has to specify the fragment length average and standard deviation for Illumina I used the code I found [here][1] on the fastq file with the forw ...
illumina assembly masurca pacbio fastqc written 5 weeks ago by nanoide30
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Comment: C: Question about exon/intron counting in RNA-seq dataset analysis
... Thank you for your useful answer! Will take it into account. Regards ...
written 6 weeks ago by nanoide30
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Question about exon/intron counting in RNA-seq dataset analysis
... Hi, So I'm currently analyzing some RNA-seq datasets and wanted to get expression at the gene level. So I got raw counts with featureCounts and then got normalized counts using DESeq2. My question is, I have huge genes with very high introns. I'm afraid the normalization is taking into account the ...
htseq-count featurecounts rna-seq written 6 weeks ago by nanoide30 • updated 6 weeks ago by swbarnes25.8k
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Comment: A: MACS2 --SPMR and --nolambda usage for version 2.1.2
... Hi, so I'm aware a few months have gone by but the Building signal track tutorial still shows --SPMR and there is the inconsistency that you explained above and wasn't commented. Any thoughts on this? Is the use of --SPMR in that context not correct anymore and the tutorial should be updated? And ...
written 9 weeks ago by nanoide30
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Is it possible to control the coordinate of the peak that HOMER takes into account to annotate?
... Hi, So I'm currently annotating some ChIP-sek peaks (coming from macs2 peak calling) using HOMER. I have observed that the "Distance to nearest TSS" column is computed using the center of the peak. My question is, is it possible to change the coordinate of the peak that HOMER uses to give a distan ...
macs2 homer peaks chip-seq annotation written 9 weeks ago by nanoide30 • updated 9 weeks ago by jared.andrews072.5k
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Comment: C: Running STAR aligner with paired-end and single-end reads simultaneously
... Hi, thanks for your responses. This is indeed the same library sequenced two different ways. I'll check out BBmap suite, thanks ...
written 10 weeks ago by nanoide30
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Comment: A: Running STAR aligner with paired-end and single-end reads simultaneously
... Thank you all for your responses. Please allow to ask for a couple of clarifications: * I get STAR cannot deal with paired-end sequencing and single-end sequencing of different length at the same time. Do you know any aligner that can? * Do you know of any published paper that have done something s ...
written 10 weeks ago by nanoide30
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Comment: C: Getting motif instances corresponding to regions
... Thanks, appreciate it! ...
written 10 weeks ago by nanoide30
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Converting motif databases from meme suite to other formats
... Hi So in order to use some TF footprinting format I'm interested in obtaining motif files in .pwm format, in the old jaspar format (before 2016). I have found that the motifs that are contained in the meme suite (http://meme-suite.org/db/motifs) can be downloaded from http://meme-suite.org/meme-sof ...
meme format motif written 10 weeks ago by nanoide30 • updated 10 weeks ago by Alex Reynolds28k

Latest awards to nanoide

Supporter 3 months ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For ATAC-seq macs2 peak calling bampe mode extension shift

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