User: rob.costa1234

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rob.costa1234140
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Posts by rob.costa1234

<prev • 93 results • page 1 of 10 • next >
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mitichondrial marker genes in SCRNAseq
... I am working on ScRNAseq and am using Saurat package. On the page http://satijalab.org/seurat/pbmc3k_tutorial.html there is mention of mitochondrial genes- mito.genes <- grep(pattern = "^MT-", x = rownames(x = pbmc@data), value = TRUE) Is there a list of mitochondrial marker genes? Any pointer ...
rna-seq written 5 weeks ago by rob.costa1234140 • updated 5 weeks ago by igor5.0k
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Comment: C: Z score in RNAseq
... Great! I was missing K means point. ...
written 5 weeks ago by rob.costa1234140
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Z score in RNAseq
... I am trying calculate Z score of expression from RANseq dataset Ultimate goal is to generate similar figure as in Supplementary Fig 2 B and C of https://www.nature.com/articles/nature24489 I read a discussion (https://www.biostars.org/p/144765/) that Z score may not be useful in showing the expres ...
rna-seq zscore written 5 weeks ago by rob.costa1234140 • updated 5 weeks ago by Kevin Blighe11k
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10x genomics scRNA converting bam per cell
... I have scRNA seq data for three time points. I ran cell ranger pipeline that gives me one bam file I want to convert this bam to one bam per sample/cell. Is there a package or toll that can help to achieve this. ...
rna-seq written 7 weeks ago by rob.costa1234140 • updated 6 weeks ago by Kevin Blighe11k
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free software or tools for analyzing mass spectrometry
... Is there any free web based or online tool to analyze mass- spec protein data? Thanks ...
proteomics written 8 weeks ago by rob.costa1234140 • updated 8 weeks ago by hlfzeus10
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single cell RNA-seq 10X genomics
... I am getting some single cell RNA-seq data for different time points. Is there a standard work flow reported for such analysis? I know there are various packages for downstream analysis of scRNA like moncol but do we process 1X data in regular RNA seq or there are special preprocessing steps involve ...
rna-seq written 9 weeks ago by rob.costa1234140
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moncole input of cufflink
... I am trying to use single cell RNA seq (SE) data using moncole @ http://cole-trapnell-lab.github.io/monocle-release/docs/#installing-monocle I aligned data to GRCH38 run cufflink, However I could not find the input file that monocole will take? Does any one in forum know which input file transcript ...
rna-seq written 11 weeks ago by rob.costa1234140
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Comment: C: general question about strand D and R
... If I quary Myc to etract upstream/ downstream -2000 bp sequence in RSAT (http://rsat.sb-roscoff.fr/retrieve-ensembl-seq_form.cgi) the first few lines are: >Homo_sapiens-ENSG00000136997-MYC-ENST00000259523 ENSG00000136997-ENST00000259523; upstream from -2000 to -1; size: 2000; locatio ...
written 3 months ago by rob.costa1234140
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general question about strand D and R
... I have a very simple question- if after genomics coordinate letter D and R mentioned, that means D is forward strand, R is reverse strand? AM I correct? Thanks ...
sequence written 3 months ago by rob.costa1234140 • updated 3 months ago by glihm530
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variant calling by GATK question about alignment
... I have a human whole genome sequence data and I would like to call SNPs/ Indels/ mutations using GATK best practice module. Can I use Bowtie 2 for alignment. Which particular genome I have to use, Does GATK work with GRCH38 or hg19. I have tried to use hg19 as reference genome and GATK gave and erro ...
gatk alignment written 3 months ago by rob.costa1234140 • updated 3 months ago by ijaz786besanttech0

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