User: nanoide

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nanoide30
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Posts by nanoide

<prev • 49 results • page 1 of 5 • next >
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HaplotypeCallerSpark How to use
... Hi all. So I wanted to try the HaplotypeCaller Spark implementation in GATK4. I'm aware it's beta and not totally recomended yet, but we want to try it. So I wanted to ask about the usage, I looked for documentation but I'm not clear on some errors I'm getting. I also wanted to ask about the --stri ...
gatk snp written 6 days ago by nanoide30 • updated 6 days ago by zx87548.2k
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Comment: C: Merging the output of salmon for RNA-seq counting with paired-end and single-end
... Thank you all for useful suggestions ...
written 27 days ago by nanoide30
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Merging the output of salmon for RNA-seq counting with paired-end and single-end reads simultaneously
... Hi all So, I'm working with some RNA-seq raw reads, both paired end (2 x 150 bp) and single-end (1x75 bp). These are coming from the same samples, but sequenced differently in 2 rounds. I want to get counts for each at the trasncript level using salmon. For DEseq2 differential expression analysis ...
paired-end salmon rna-seq single-end written 27 days ago by nanoide30
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Peak annotation with HOMER. Statistics with the annStats parameter
... Hi all. So I've been annotating some peaks with HOMER annotatePeaks. I have followed the instructions in the [webpage][1] for changing the TSS definition: *Although HOMER doesn't allow you to explicitly change the definition of the region that is the TSS (-1kb to +100bp), you can "do it yourself" b ...
homer annotatepeaks.pl stats chip-seq written 7 weeks ago by nanoide30
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Question about HOMER peak annotation to some features. Customize gff3?
... Hi all So I'm currently annotating some ChIP-seq peaks using HOMER annotatePeaks.pl and a gff3 file with the features for my organisms. It seems to be working fine. The features that HOMER is annotating are: "TTS", "Exon", "Intron", "Intergenic" and "Promoter-TSS". But the column of Detailed Annota ...
homer chip-seq annotation written 8 weeks ago by nanoide30
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Comment: C: samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
... Thank you both for the comments, regards ...
written 8 weeks ago by nanoide30
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Comment: C: samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
... Thanks for the insights! Regards ...
written 8 weeks ago by nanoide30
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samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
... Hi there, So I'm currently analyzing some ATAC-seq data. The duplicated reads were removed using first samtools fixmate -m and then samtools markdup -rs. I'm facing many discarded reads and I cannot repeat this step anymore, maybe in the future. I was wondering, are there any known differences betw ...
samtools atac-seq markduplicates written 8 weeks ago by nanoide30 • updated 8 weeks ago by predeus1.2k
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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 months 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 4 months ago by nanoide30

Latest awards to nanoide

Popular Question 3 months ago, created a question with more than 1,000 views. For Can I convert normalized counts from DESEQ2 into fpkm?
Supporter 6 months ago, voted at least 25 times.
Popular Question 11 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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