User: Moneeb Bajwa

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Posts by Moneeb Bajwa

<prev • 43 results • page 1 of 5 • next >
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Comment: C: Connect gene names to GO terms/function for loading in DESeq2
... Thank you. But how would I get the GO annotations for that? I tried a couple websites like https://go.princeton.edu/cgi-bin/GOTermFinder but I don't understand why it doesn't give me any results? I just put like RP23-115I1.6 and select mouse genome it should return something right? It didn't work. ...
written 3 months ago by Moneeb Bajwa0
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Comment: C: Connect gene names and GO terms after STAR for DESeq2
... Also, why didn't you just use `merge()`? ...
written 3 months ago by Moneeb Bajwa0
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Comment: C: Connect gene names and GO terms after STAR for DESeq2
... Hello Moneeb Bajwa! We believe that this post does not fit the main topic of this site. I have created a new post to address the remaining unanswered part to this question: Connect gene names to GO terms/function for loading in DESeq2 For this reason we have closed your question. This allows us ...
written 3 months ago by Moneeb Bajwa0
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Connect gene names to GO terms/function for loading in DESeq2
... Hi, I would like to connect the gene names to GO terms and function before loading them into DESeq2. The counts are from single-end mouse reads mapped to the genome and annotation files from GENCODE. The counts files I have look like this right now: gene_id counts gene ...
annotation go terms deseq2 rna-seq R written 3 months ago by Moneeb Bajwa0 • updated 3 months ago by prakash520
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Comment: C: Connect gene names and GO terms after STAR for DESeq2
... Thank you greatly. Regarding the GO terms and functional annotation I had mentioned, how would that come into play? The paper I am using mentions that they performed functional annotation with DAVID; my goal is to reproduce a figure similar to Figure D in the link. In the paper, the caption for that ...
written 3 months ago by Moneeb Bajwa0
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Comment: C: Low alignment with Trinity but high alignment in SAM files
... I had some more questions regarding that which I just made into a separate post here: https://www.biostars.org/p/329607/ ...
written 3 months ago by Moneeb Bajwa0
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(Closed) Connect gene names and GO terms after STAR for DESeq2
... **EDIT**: I have created a new post to address the remaining unanswered part to this question: https://www.biostars.org/p/330049/ Hi, I want to ask how to go about doing differential expression analysis after getting gene counts with STAR. I would also like to connect the gene names to GO terms bef ...
go terms alignment deseq2 rna-seq star written 3 months ago by Moneeb Bajwa0
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Comment: C: Low alignment with Trinity but high alignment in SAM files
... This is the code I used: #!/bin/sh STAR --runThreadN 5 --runMode genomeGenerate --genomeDir genome_dir \ --genomeFastaFiles gencode.vM18.transcripts.fa \ --sjdbGTFfile gencode.vM18.annotation.gtf \ --limitGenomeGenerateRAM 95444909440 \ 1>prepStar.log 2>prepStar.err &a ...
written 3 months ago by Moneeb Bajwa0
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Comment: C: Low alignment with Trinity but high alignment in SAM files
... Maybe I am using the wrong genome files? I should select the ones labelled PRI from this link right?: https://www.gencodegenes.org/mouse_releases/current.html ...
written 3 months ago by Moneeb Bajwa0
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Comment: C: Low alignment with Trinity but high alignment in SAM files
... This is what I did: #!/bin/sh STAR --runThreadN 5 --runMode genomeGenerate --genomeDir genome_dir \ --genomeFastaFiles gencode.vM18.transcripts.fa \ --sjdbGTFfile gencode.vM18.primary_assembly.annotation.gtf \ 1>prepStar.log 2>prepStar.err & ...
written 3 months ago by Moneeb Bajwa0

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