User: asmariyaz23

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asmariyaz2310
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United States
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7 months, 1 week ago
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6 years, 6 months ago
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Posts by asmariyaz23

<prev • 13 results • page 1 of 2 • next >
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Annotating variants called with NanoVar with Annovar
... Hello, I am trying to annotate SVs that I got by running NanoVar using Annovar (build hg38). Here are the commands I used to run Annovar. annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/ annotate_variation.pl -buildver hg38 -downdb cytoBand humandb/ anno ...
annotation next-gen sequence written 8 months ago by asmariyaz2310 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: makeblastdb and windowsmaker error
... MDB_NOTFOUND error refers to some sort of EOF error according to [docs][1] here. [1]: http://www.lmdb.tech/doc/group__errors.html#gabeb52e4c4be21b329e31c4add1b71926 ...
written 9 months ago by asmariyaz2310
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Comment: C: makeblastdb and windowsmaker error
... I played around with 2 scenoarios: # Moved the fasta file mv hg38.fa hg38.fa.blastdb /scratch/SOFTWARE/ncbi-blast-2.10.0+-src/c++/ReleaseMT/bin/blastdbcheck -db hg38.fa.blastdb -verbosity=3 Writing messages to at verbosity (Detailed) ISAM testing is ENABLED. Legacy testing ...
written 9 months ago by asmariyaz2310
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makeblastdb and windowsmaker error
... I want to run an aligner, [HS-BLASTN][1] for which, I need to run makeblastdb and windowmasker. I ran makeblastdb using fasta file downloaded with rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz, without any apparent errors: /scratch/SOFTWARE/ncbi-blast-2.10.0+-sr ...
software error genome alignment written 9 months ago by asmariyaz2310
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Plot features on tsne plot with high pLi scores
... Hello, I have used Seurat to obtain tsne plot and calculated the DE genes for each cluster. I have pLi scores for each of these DE genes and I want to somehow plot the genes that have pLi score >=0.9 on them. Using FeaturePlot in Seurat I could do 1 gene per plot but I was wondering if there is ...
pli genes tsne rna-seq seurat written 11 months ago by asmariyaz2310 • updated 11 months ago by Biostar ♦♦ 20
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Comment: A: Gene set enrichment analysis using a curated gene list and cluster DE genes
... I will try it this way as well, just needed clarification on 2 variables N and k. N = Are these the total number of genes in matrix (after initial filtration in a single cell package, in my case Seurat)? k = Here do you refer to only the DE expressed genes in the cluster of interest or the total ...
written 12 months ago by asmariyaz2310
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Gene set enrichment analysis using a curated gene list and cluster DE genes
... I have a curated gene list using which I would like to carry out enrichment analysis on DE genes in clusters obtained using Seurat. I first tried to do this manually using Fisher Exact test like so: No. genes in curated list: 5840 No. DE genes in Cluster 0 (from Seurat): 512 No. Over ...
enrichment rna-seq R written 12 months ago by asmariyaz2310
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Answer: A: Seurat cluster is split and appears in 2 different areas on the tsne plot
... I have been trying to play with tsne parameters as you suggested, mainly max.iter, min_dist and n_neighbors. For some reason it is the 13th cluster which splits up and occurs in 3 different locations. Image in link below. Is there some other parameter that I should explore? ![enter image descriptio ...
written 13 months ago by asmariyaz2310 • updated 13 months ago by i.sudbery8.5k
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Seurat cluster is split and appears in 2 different areas on the tsne plot
... Hello, I am analyzing a single cell dataset using Seurat. The tsne plot obtained shows the same cluster in 2 different locations. I am wondering if I should be merging them or play with the parameters for tsne to separate them out further. To study these 2 clusters I want to look into the genes in ...
R tsne seurat cluster_analysis written 13 months ago by asmariyaz2310
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Answer: A: Converting Between Mass-Spec Database Search Result Formats (Specifically Pep.Xm
... I don't know too much about R but Python's XML parser does an excellent job in doing what you want. Once you know the fields within this id.csv file that ISOBAR accepts, extract the information with the parser, store them as lists and push them to a writing file, Please ignore this post if Python i ...
written 6.4 years ago by asmariyaz2310

Latest awards to asmariyaz23

Great Question 5.0 years ago, created a question with more than 5,000 views. For Convert Distance Matrix To Newick Format- Biopython
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Newick Tree Reordering
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Convert Distance Matrix To Newick Format- Biopython

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