User: rajpal22288

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rajpal2228850
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Posts by rajpal22288

<prev • 29 results • page 1 of 3 • next >
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Comment: C: What are the best quantification tools for miRNA seq?
... Did you check the contamination with FASTQ-Screen? ...
written 4 days ago by rajpal2228850
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Comment: C: What are the best quantification tools for miRNA seq?
... Okay, let's assume that the trimming was perfect. Can you try this workflow? 1. Build Index using Bowtie2 2. Bowtie2 Mapping 3. Index (using Bowtie2) 4. remove duplicates using UMI-dedup 5. Count using Htseq try it with 1 or 2 fastq files and If the problem still persists, then please ask th ...
written 9 days ago by rajpal2228850
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Comment: C: What are the best quantification tools for miRNA seq?
... Can you mention the whole workflow you followed? starting from trimming and adapter removal! We had the same problem, but it was one of the parameters in UMI-tools that gave us low reads. ...
written 9 days ago by rajpal2228850
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Answer: A: Web-based tool for 3D visualization of proteins given a .pbd file
... But, why do you want to visualize PDB files online? There are pretty good offline tools for this purpose (Chimera, Pymol). However, if you still prefer web-based tools, Protein-Ligand Interaction Profiler (PLIP) is a good one. ...
written 10 days ago by rajpal2228850
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Comment: C: Selecting Samples based on Clustering
... So, there were 3 types of samples. 1. Treated Nodules - 16 samples 2. Control Nodules - 3 samples 3. Untreated Nodules - 16 samples Performed Correlation clustering after DESEQ2 using Pheatmap Now, let's say, only violet samples with large cluster was selected, and the cyan cluster was compl ...
written 12 days ago by rajpal2228850
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Selecting Samples based on Clustering
... If I only select samples based on their clustering in heatmaps, am I not creating a bias ? For example, I had 35 samples (RNA Seq) nitially, but, in the end, we only selected 12 samples based on their clustering. When I checked for some of the genes in both cases, they were hugely varying in terms o ...
gene rna-seq sequencing written 12 days ago by rajpal2228850
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Comment: C: Error in GATK HaplotypeCaller
... Yess, found the culprit. It was the bed file indeed!! Thanks !! ...
written 10 weeks ago by rajpal2228850
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Error in GATK HaplotypeCaller
... I am getting the following error while running the following command: gatk HaplotypeCaller --java-options '-Xms2g -Xmx31g -XX:ParallelGCThreads=4 -Djava.io.tmpdir=/u/rajeshpal93/scratch/ca/diva_test_final/temp/samtools' -R /ELS/els9/users/biosciences/references/ucsc/hg19/ucsc.hg19.fasta -I read ...
genome assembly alignment snp written 10 weeks ago by rajpal2228850
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Can you also post the snapshot of the gtf file? ...
written 9 months ago by rajpal2228850
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Answer: A: How to select multiple nodes with mouse - left click and drag
... Did you try selecting the nodes by holding "Ctrl" key? ...
written 9 months ago by rajpal2228850

Latest awards to rajpal22288

Popular Question 9 months ago, created a question with more than 1,000 views. For UMI Tools Dedup
Scholar 15 months ago, created an answer that has been accepted. For C: Unable to convert txt to gtf format

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