Moderator: Friederike

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Friederike5.9k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

http://abc.med.cornell.edu/

Posts by Friederike

<prev • 723 results • page 1 of 73 • next >
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Comment: C: TSS metaprofile using Deeptools
... The error most likely occurred because you didn't include any entry with "transcript" in the 3rd column in your test.gtf. > But now I am doubting whether setting --transcript ID gene and --transcript_id_designator gene_id is in in this specific case correct (trying to get the signal over entire ...
written 5 days ago by Friederike5.9k
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Comment: C: BWA mem and Samtools sort in Bash script
... do you have to load `samtools` first, e.g. via spack or the like? I.e. when you log into your server can you use `samtools` right away? also, can you post the entire script? ...
written 11 days ago by Friederike5.9k
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Comment: C: RNA seq data analysis
... I'm confused. You know or you do **not** know how to download data from SRA? ...
written 19 days ago by Friederike5.9k
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Comment: C: RNA seq data analysis
... It is usually easier to download the data deposited in the SRA via either [GEO](https://www.ncbi.nlm.nih.gov/gds) or [ENA](https://www.ebi.ac.uk/ena/browser/home) ...
written 20 days ago by Friederike5.9k
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Comment: C: Every time the results of findMotifGenome.pl in HOMER is different
... sorry, can't help with this, but you can check the biostars archive whether anyone has asked that question already (i.e. "How can I mimick the background selection by HOMER?" or the like) and if you don't find what you're looking for, just post it as a new question ...
written 20 days ago by Friederike5.9k
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Comment: C: Read in UMI count table from GEO for use in Seurat pipeline
... I've put the results of the following lines of code [here](https://wcm.box.com/s/2shs8kr0rg5y4qdfgyaq9zoy4t6mvlgd), let me know if that works for you. ``` sparse.mat <- Matrix(as.matrix(tt[, -1, with=FALSE]), sparse=TRUE) DropletUtils::write10xCounts("GSM2781556", x = sparse.mat, gene.id= tt$V1) ...
written 21 days ago by Friederike5.9k
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Comment: C: Read in UMI count table from GEO for use in Seurat pipeline
... Maybe this helps: ``` > library(data.table) > tt <- fread("https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2781nnn/GSM2781556/suppl/GSM2781556_Dropseq_120000_umi.txt.gz") [100%] Downloaded 40425751 bytes... Warning message: In fread("https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2781nnn/GSM2 ...
written 21 days ago by Friederike5.9k
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Comment: C: MACS sampling down
... Yes. However, MACS is usually doing the library size correction internally, there shouldn't be a need for you to downsample manually AFAIK ...
written 21 days ago by Friederike5.9k
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Comment: C: Gene count vs Relative gene abundance
... I am no metagenomics expert, but I could see how Metaphlan may simply have not been an established tool while Chatelier et al were working on their analyses. The first Metaphlan paper seems to have been published in 2012, not sure if people were aware of it beforehand. I'm sure there are other reaso ...
written 21 days ago by Friederike5.9k
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Answer: A: Gene count vs Relative gene abundance
... >What does this threshold level refers to? I would interpret "threshold of one read for gene identification" so that a given gene had to have at least one sequenced read in order for it to be retained for downstream analyses. In other words, all genes for which at least one sequencing read was f ...
written 21 days ago by Friederike5.9k

Latest awards to Friederike

Commentator 5 days ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Understanding ATAC-seq data
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 11 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Scholar 4 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Student 6 months ago, asked a question with at least 3 up-votes. For Understanding ATAC-seq data
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Scholar 9 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 12 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ

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