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Comment: Gene Specific coverage from WGS data
Answer: ATAC-Seq and RPKM
Answer: MSA and distance matrix in R
Comment: MSA and distance matrix in R
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
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Recent Replies
Answer: What is the proper way to identify the cell types of scRNAseq cluster?
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I will say that the proper way is the one that confidently identifies your celltypes. > optimal number of marker genes to consider. T…
Comment: How to compute TPM normalized values for TCGA miRNA data?
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When everything is the same size, correcting for size is pointless. It doesn't change the numbers much at all.
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What do the alignments look like in IGV?
Comment: HCL database download
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sooni
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I solved the problem! Thanks!
Comment: Gene Specific coverage from WGS data
by
Adyasha
• 0
Thank you, here I am giving you some example , suppose I have bam files . 1.bam 2.bam 3.bam 4.bam now I want to see Spike gene coverage in …
Answer: Bioinformatics Analyst - Laboratory Medicine and Pathology
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I'm having a problem and I can't find the button to post, how do you post?
Comment: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
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MICOS
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Contest question details: **To effectively address the accuracy and efficiency issues of clustering algorithms used for spatial transcript…
Comment: HCL database download
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sooni
▴ 20
I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
Comment: Understanding STAR output (Aligned.out.sam file)
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GenoMax
142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
Answer: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom
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LChart
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Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
Comment: Where to get the following bed file?
by
GenoMax
142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file?
by
LChart
3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
Ngrin
• 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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Chris Dean
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It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function
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bk11
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Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
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