User: N15

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N15120
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Posts by N15

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How can a single peptide produce redundant fragments during mass spec proteomics?
... I am wondering how a single ionized peptide can produce fragments offset by one amino acid, as shown in this figure: ![enter image description here][1] For instance, if your peptide is ANELLLNVK, I could understand producing fragments ANEL and LLNVK for example, but how A, AN, ANE, ANEL etc? How c ...
proteomics mass spectrometry written 3 months ago by N15120
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Comment: C: How to combine different data types and perform PCA in R
... I'm not sure how valid it is to ordinate using different sequencing types, because you might see separation based primarily on method and not on a biologically meaningful differences. But, you could try and see what it looks like I suppose. I would ensure the samples are normalized using the same me ...
written 4 months ago by N15120
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Comment: C: Which bioinformatic tool can I use to assess overlapping genes between 2 dataset
... Are you working with a genome? Transcriptome? How were they processed? Is it an assembly? Usually assemblies reduce redundancy by removing identical contigs. Are you working with peptides or spectral counts? What tools are you currently using the examine the proteome? ...
written 4 months ago by N15120
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Comment: C: BLAST Command Not Found Under Parent Directory
... I would recommend installing with conda, if you aren't already. It has taken care of almost all of my $PATH issues. https://anaconda.org/bioconda/blast ...
written 4 months ago by N15120
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Answer: A: Mapping an unique KEGG pathway
... Look into the R package clusterProfiler: https://yulab-smu.github.io/clusterProfiler-book/chapter6.html ...
written 4 months ago by N15120
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Comment: C: gene expression comparison between tpm and fpkm
... You could compare genes within one dataset, i.e., Gene A across samples within the TPM dataset and Gene A across samples from the FPKM data set, but I would NOT directly compare normalized values between the FPKM and TPM data sets. Get the raw count data and ensure they are normalized in the same ma ...
written 4 months ago by N15120
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Answer: A: Heatmap of Distance Clusters
... pheatmap allows euclidean distance clusters among rows/columns https://davetang.org/muse/2018/05/15/making-a-heatmap-in-r-with-the-pheatmap-package/ ...
written 4 months ago by N15120
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Answer: A: Custome database creation from RNAseq dataset for proteomics database search hel
... You need to assemble the transcriptome, and then translate into amino acid space. This can then be used as the fasta database you search against to assign PSMs. Trinity is one of the top performing assemblers, perhaps you should give it a try: https://github.com/trinityrnaseq/trinityrnaseq/wiki ...
written 4 months ago by N15120
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Comment: C: using heat map to measure gene expression at different developmental stages
... Try log transforming your count matrix before plotting with heatmap. You can export log-transformed counts from edgeR directly: tmm<-cpm(dge, normalized.lib.size=T, log=T) ...
written 4 months ago by N15120
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Comment: C: How to rarefying 18s rDNA data?
... You plot it before rarefying. I suggest following tutorials to do this: https://rpubs.com/brouwern/iNEXTvVEGAN ...
written 4 months ago by N15120

Latest awards to N15

Supporter 4 months ago, voted at least 25 times.
Scholar 4 months ago, created an answer that has been accepted. For A: Custome database creation from RNAseq dataset for proteomics database search hel
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Custome database creation from RNAseq dataset for proteomics database search hel

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