User: Folder40g

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Folder40g110
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Posts by Folder40g

<prev • 29 results • page 1 of 3 • next >
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rsem matrix to DESeq2
... I know that I can pass the gene-level rsem matrix to limma and work with it. But can I use it in DESeq? I've a rsem matrix from firebrowse, gene-level ~20000 rows. DESeq requires raw counts, and as I only have the matrix with samples/gene I can't use tximport(). Thanks ...
rsem written 10 days ago by Folder40g110 • updated 10 days ago by Kevin Blighe21k
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Comment: C: Question: Unmapped reads at TCGA bam files
... Yes, it seems thats what is happening. A "bug" from STAR aligner. ...
written 7 weeks ago by Folder40g110
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Question: Unmapped reads at TCGA bam files
... I haven't use samtools for a while and now I've some files from TCGA from which I'm checking the reads. I'm trying to see if there are any unmapped sequences at TCGA bam files: `samtools view -f 4 file_gdc_realn_rehead.bam` and I get this `UNC-SN:197:C0XX:4:204:155:805 69 chr1 14496 0 * = 14496 0 A ...
tcga bam written 7 weeks ago by Folder40g110 • updated 7 weeks ago by toralmanvar350
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Comment: C: Meaning letters in TCGA sample barcode field
... Thanks I was trying to get that image. ...
written 7 weeks ago by Folder40g110
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Meaning letters in TCGA sample barcode field
... Hi, I've a doubt for which I've no answer. The fourth field of the TCGA barcode contains the information about the sample, either primary tumor, metastatic, etc For instance `TCGA-93-A4JP-01A-11H-A24S-13`, this is a primary tumor, but what does the A next to the 02 means? Sometimes I've sen other ...
barcode tcga written 7 weeks ago by Folder40g110 • updated 7 weeks ago by Kevin Blighe21k
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Inferring gene network
... Hi I would like to infer the gene network from the gene X to its secretome. I've a RNAseq DEG analysis (gain of function for the gene X), and also the secretome of this gene. Using the differentially expressed genes from my DEG analysis as a signature I have been able to split in two cohorts (by ...
gene network aracne written 6 months ago by Folder40g110
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Raw counts TCGA Firebrowse
... Hi I've downloaded some data from firebrowse. I know some data is in RSEM format. But my question is. Why a file such `SKCM.uncv2.mRNAseq_raw_counts.txt`, which in theory is just the raw counts it contains decimals? I would expect decimals in normalized and RSEM but not in the raw data. Just want ...
tcga counts firebrowse written 8 months ago by Folder40g110 • updated 8 months ago by Kevin Blighe21k
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CRISPR screening analysis using mageck
... Hi I've some fastq of a CRISPR screening analysis, with replicas. I'm doing some testing before the analysis. I've done it twice -removing and keeping the adapters-, in both cases when I used the option mageck count there is a warning that shows up in the screen for most of the samples. All fastq h ...
crispr reads mageck screening written 9 months ago by Folder40g110
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Answer: A: Software For Hla Typing Using Ngs?
... Sorry for reviving back this topic. My question is: Does anyone knows a data set with RNAseq for which the HLA typing has been performed by a precise method (PCR for instance)? I would like to check a software but I've not been able to find in any paper (HLAmine, seq2HLA, optitype, etc) that the d ...
written 10 months ago by Folder40g110
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svaseq and combat
... Hi I have samples (rnaseq) coming from two different experiments. I plotted all samples in a PCA plot and I saw a clear batch effect. Then I used `svaseq` to plot a PCA without the batch effect and I got something quite reasonable, samples from different experiments mix but without a clear order. S ...
combat sva effect batch written 13 months ago by Folder40g110 • updated 11 months ago by Biostar ♦♦ 20

Latest awards to Folder40g

Student 6 months ago, asked a question with at least 3 up-votes. For Raw counts TCGA Firebrowse
Popular Question 8 months ago, created a question with more than 1,000 views. For Skip orientation RF
Popular Question 13 months ago, created a question with more than 1,000 views. For Bimodal GC content
Popular Question 19 months ago, created a question with more than 1,000 views. For Bimodal GC content
Appreciated 20 months ago, created a post with more than 5 votes. For Bimodal GC content
Student 2.4 years ago, asked a question with at least 3 up-votes. For Bimodal GC content

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