User: simang5c

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simang5c10
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Posts by simang5c

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Knock out genes and TPM
... Thanks for the comment @jordi. Yes, we performed differential expression analysis as well. However, the main question that came up after observing the TPM values of deleted genes in mutant and Wild was, if the gene is knocked out, its TPM values should be 0 (ideal case) or less than 1 TPM in all sam ...
written 7 weeks ago by simang5c10
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Comment: C: Knock out genes and TPM
... Sorry, I'll try sharing some more details. We have 3 fungal strains from which we knocked out single-copy genes using Split-Marker Recombination. We then performed Transcriptomics sequencing and completed the bioinformatics analysis. We used STAR for aligning and RSEM for quantification. Following ...
written 7 weeks ago by simang5c10
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Knock out genes and TPM
... why do deleted genes still show significant TPM? In some cases even higher than the wild type? I checked the alignment using IGV viewer but couldn't find much difference, any help would be much appreciated. Thanks in advance! ...
gene alignment next-gen rna-seq gene knock outs written 7 weeks ago by simang5c10
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Comment: C: RNA-Seq Data analysis FPKM values mostly showing 0
... Thank you so much.. I will look into it! ...
written 3.6 years ago by simang5c10
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RNA-Seq Data analysis FPKM values mostly showing 0
... Hi Everyone! I have Human RNA-Seq data downloaded from NCBI, for which I am performing data analysis. I aligned the reads using tophat2 by providing the premade indices from GRCh38.fa and GRCh38.chr.gtf. After aligning and assembling with Cufflinks when I checked the transcripts.gtf file; most FPKM ...
assembly rna-seq rseqc written 3.7 years ago by simang5c10
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Seed and Kegg analysis in Megan 5
... Hi everyone I have a BlastNT.xml file and I tried to perform KEGG and Seed analysis using the kegg and seed mapping files gi2kegg-Aug2016X-ue.bin, gi2seed.map respectively. Since It Is a BlastNT file there is no Ref SEQ Id. I used the GI id. Setting Min score as 50, Min support 1 and LCA percent ...
metagenomics ngs megan written 3.8 years ago by simang5c10

Latest awards to simang5c

Popular Question 3.4 years ago, created a question with more than 1,000 views. For RNA-Seq Data analysis FPKM values mostly showing 0
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Seed and Kegg analysis in Megan 5

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