User: khorms

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khorms110
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Moscow
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22 hours ago
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6 years, 11 months ago
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Posts by khorms

<prev • 38 results • page 1 of 4 • next >
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Answer: A: Syntax for samtools flagstat on multiple .bam files outputting to .txt file
... An easy way of doing it is to run samtools flagstat on multiple .bam files and then combine their output together using [multiqc][1] So something like samtools_stat_commands=() samtools_stat_log_folder='' multiqc_folder='' for i in ${aligned_folder}/*.bam do sample_name=$(basename $ ...
written 12 days ago by khorms110
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Answer: A: Blood Derived Normal RNA_seq samples TCGA
... I don't think there are any. In order to double check, you could do this: This [table][1] show the codes for sample types; so all you need to know to figure out what kind of sample you are looking at is the last two digit barcode. You could go to [Xena][2], look at the pages corresponding to the ...
written 14 days ago by khorms110
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Answer: A: Test if a list of genes with coordinates are expressed (hisat2 data)
... You could use [IGV][1] to visualize both your alignment .bam file and your bed file; this way you could manually inspect the regions of interest [1]: http://software.broadinstitute.org/software/igv/ ...
written 14 days ago by khorms110
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Answer: A: Pysam pileup method gives more columns than expected
... pysam pileup chooses all the reads that align to the selected region, then iterates through all the positions covered by these reads. Therefore, it's expected that the value you get in the end for counter is larger than 100 (since some reads extend beyond the region you have specified). I am not sur ...
written 15 days ago by khorms110
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Alzheimer's datasets highlighting role of individual genes
... A question to the folks who studies Alzheimer's disease here. My colleagues and I have developed a new program that predicts the master regulators based on transcriptomic changes (yes, another one). We have applied it to Alzheimer's disease RNAseq datasets and we have identified several potential m ...
alzheimer's data rna-seq sequencing written 15 days ago by khorms110 • updated 15 days ago by ATpoint36k
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Comment: C: computing resources for scRNA-seq analysis
... Are you talking about the initial preprocessing (like 10X's CellRanger) or downstream analysis? Which tool did you use that didn't like the 64G limit? I know that CellRanger by default tries to use 90% of all memory on the machine and therefore causes troubles; you have to explicitly specify the amo ...
written 16 days ago by khorms110
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Answer: A: GSVA analysis between Clusters
... I am not sure about Seurat but another very popular single cell analysis framework Scanpy allows you do perform GSVA analysis with tools like [diffxpy][1] [1]: https://diffxpy.readthedocs.io/en/latest/api/index.html#gene-set-enrichment-enrich ...
written 16 days ago by khorms110
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Answer: A: Entrez e-utils reference for ensembl ids
... Can't you just download biomaRt tables and use them to look up the correspondence like it's done [here][1]? [1]: https://stackoverflow.com/questions/53339481/entrez-gene-ids-from-gene-list-using-biomart ...
written 19 days ago by khorms110
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Answer: A: How to generate a mouse reference genome in STAR?
... In the Ensembl link you attached, there are files that are named something-something-"assembly", for example Mus_musculus.GRCm38.dna.primary_assembly - that is what you need ...
written 19 days ago by khorms110
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Comment: C: Trouble quantifying scRNAseq experiment
... The authors say in the Methods section that they used CellRanger to process their sequencing reads. Is there any particular reason (bseides speed) why you are using Salmon? As far as I know it's a standard practice to use CellRanger software when working with 10X data, and I wouldn't always expect S ...
written 10 weeks ago by khorms110

Latest awards to khorms

Scholar 19 days ago, created an answer that has been accepted. For A: How to generate a mouse reference genome in STAR?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Getting upstream of a given gene from a .gbk file
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Downloading genes annotations from UCSC Table Browser
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Visualisation of clusters produced by mothur
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to get the abundance of genes in metagenomes from MG RAST
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How to get the abundance of genes in metagenomes from MG RAST
Popular Question 4.2 years ago, created a question with more than 1,000 views. For getting data from american gut project
Popular Question 5.5 years ago, created a question with more than 1,000 views. For How to get the abundance of genes in metagenomes from MG RAST

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