User: tiago211287

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tiago2112871.2k
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Posts by tiago211287

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Comment: C: Setting/finding the log odds detection threshold in custom homer PWMs
... good unanswered question ...
written 8 weeks ago by tiago2112871.2k
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Comment: C: Unzipping SAM files
... Do you want to make a SAM become a FASTA? Did you gzip the SAM files? It would be more convenient if they were converted to a BAM file. check http://seqanswers.com/forums/showthread.php?t=6169 What you want might be done by: cat filename.sam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > ...
written 11 weeks ago by tiago2112871.2k • updated 11 weeks ago by RamRS30k
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Comment: C: What is difference between bulk RNAseq and mRNAseq?
... I guess I am in a bubble then. 99% of RNA-Seq is made out of sorted cells on my planet, and we called it Bulk RNA-Seq. RNA-Seq obtained from entire tissues is referred to as just RNA-Seq. But I guess it makes sense that Bulk could also be referred to tissue, although I have associated Bulk as a more ...
written 11 weeks ago by tiago2112871.2k
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Comment: C: What is difference between bulk RNAseq and mRNAseq?
... Bulk Rna-seq is a more commonly used term to refer to a sample of sorted cells (using FACS) to select a more homogeneous cell population than using a tissue slice for RNA extraction. ...
written 11 weeks ago by tiago2112871.2k
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Comment: C: Denovo assembly or Reference based assembly for identifying novel lncRNAs
... I don't know stringtie so I can't really answer your question. As a suggestion, one good approach is to use Trinity to denovo assembly your transcriptome. Later you can align the FASTA file containing transcripts against the full transcriptome annotation that can be found in gencode. All nonmatch t ...
written 12 weeks ago by tiago2112871.2k
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Comment: C: How can I add sequences to my BED file?
... Maybe if you give us a sample of your input we could try to reproduce the phenomena. ...
written 12 weeks ago by tiago2112871.2k
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Answer: A: Differential Gene Expression Using Deseq2
... The count matrix is a non-normalized data format. If you are using Deseq2 you can extract the normalized matrix with : library(dplyr) library(DESeq2) library(ComplexHeatmap) #Extract the rlog matrix from the Deseq2 results rld <- rlog(dds, blind=FALSE) mat <- assa ...
written 12 weeks ago by tiago2112871.2k
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Answer: A: multi-factor Deseq LRT test analysis
... You can extract the LRT results with: res <- results(dds) and use the table or save it as an rds or xlsx file like: openxlsx::write.xlsx(as.data.frame(res), "LRT.xlsx", row.names = T) saveRDS(as.data.frame(res), "LRT.rds) As note: The LRT does not output a fold change value, inste ...
written 3 months ago by tiago2112871.2k
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Answer: A: Cellranger: BCR analysis
... You can use cite-seq-Count to quantify the antibody tags and generate an 10x-like output that can be easily imported to R using the Seurat package. Software: https://github.com/Hoohm/CITE-seq-Count Tutorial: https://hoohm.github.io/CITE-seq-Count/Running-the-script/ ...
written 3 months ago by tiago2112871.2k
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Comment: C: Counting single-cell ATAC fragments at peaks on BED file
... Why can't you just use your bed file with your alignment files (BAMs) by using featureCounts software to count the number of fragments in each peak region? ...
written 4 months ago by tiago2112871.2k

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