User: Folder40g

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Folder40g110
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Posts by Folder40g

<prev • 31 results • page 1 of 4 • next >
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TCGA expression data (TPM)
... I'm using a software that requieres either TPM or raw counts at gene level. So I downloaded this data set from Xena browser: https://xenabrowser.net/datapages/?dataset=TCGA.SKCM.sampleMap%2FHiSeqV2&host=https%3A%2F%2Ftcga.xenahubs.net This matrix seems to be the log2(RSEM output + 1) Am I wro ...
tcgabiolinks tcga tpm expression written 3 months ago by Folder40g110
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TCGA purity data
... Hi I know that Cosmics offers a file with the purity for each tumor sample but no BAF or LogR, but I'm interested in running ascat on some TCGA samples to obtain Germline/Tumor BAF and LogR for a downstream analysis. Do you know if there is any database with this information available? I've not fo ...
tcga ascat purity written 5 months ago by Folder40g110
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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 6 months ago by Folder40g110 • updated 6 months ago by Kevin Blighe33k
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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 months 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 months ago by Folder40g110 • updated 7 months ago by toralmanvar720
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Comment: C: Meaning letters in TCGA sample barcode field
... Thanks I was trying to get that image. ...
written 7 months 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 months ago by Folder40g110 • updated 7 months ago by Kevin Blighe33k
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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 11 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 14 months ago by Folder40g110 • updated 14 months ago by Kevin Blighe33k
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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 15 months ago by Folder40g110

Latest awards to Folder40g

Popular Question 4 months ago, created a question with more than 1,000 views. For Skip orientation RF
Popular Question 4 months ago, created a question with more than 1,000 views. For Skip orientation RF
Student 11 months ago, asked a question with at least 3 up-votes. For Raw counts TCGA Firebrowse
Popular Question 14 months ago, created a question with more than 1,000 views. For Skip orientation RF
Popular Question 18 months ago, created a question with more than 1,000 views. For Bimodal GC content
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Bimodal GC content
Appreciated 2.2 years ago, created a post with more than 5 votes. For Bimodal GC content
Student 2.9 years ago, asked a question with at least 3 up-votes. For Bimodal GC content

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