User: Sepd

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Sepd0
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Posts by Sepd

<prev • 13 results • page 1 of 2 • next >
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Change XLOC to FBtr, FBgn or any other ID that can go through DAVID
... I have a list of XLOC gene IDs from a CUFFlink output and I need to change them to any other ID that would help me understand them better. I do not have the original output so I am unable to do anything with that. I would appreciate any help. ...
galaxy xloc id conversion written 19 months ago by Sepd0
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Comment: A: converting RSEM bam output into sam files for DEseq?
... I wanted to thank everyone who responded. I decided to use tximport and then DEseq. ...
written 20 months ago by Sepd0
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Comment: C: converting RSEM bam output into sam files for DEseq?
... by transcript to gene mapping do you mean the transcript.bam output of RSEM? ...
written 21 months ago by Sepd0
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Comment: C: converting RSEM bam output into sam files for DEseq?
... RSEM gave me a transcript.bam output file. I was just reviewing my work and I remembered I am trying to convert these bam files into sam for input into htseq because of the sentence below. Will this bam output from RSEM be OK to convert into sam and input into htseq? *"Here I used BWA to align the r ...
written 21 months ago by Sepd0
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Comment: C: converting RSEM bam output into sam files for DEseq?
... Thank you for your help. Can you explain how to do this? Do I use HTSeq and my bam files from RSEM? Also is DEseq only ran on Rstudio on my local computer? Is there anyway to do it on HPC? Sorry I am a beginner. You should have a bam file of your aligned reads, no. So it's just a matter of using a ...
written 21 months ago by Sepd0
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Comment: C: converting RSEM bam output into sam files for DEseq?
... I have a gene.results but they should be normalized read counts. Is there anyway I can get this from converting the BAM file into something? I just don't have time to start over. ...
written 21 months ago by Sepd0
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converting RSEM bam output into sam files for DEseq?
... Hi everyone, I have used RSEM to calculate expression values and then used ebseq to measure differential expression. Eb seq was not helpful in throwing out transcripts that were not consistent through out replicates so now I am trying to use DEseq. I am planning on converting my transcript.bam file ...
sam bam deseq rsem rna-seq written 21 months ago by Sepd0
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Comment: C: How to filter RNAseq Data for being constant in all three biological replicates
... I am really trying to avoid doing it manually. I will try using these instead of EBseq to see of it helps filter out these faulty transcripts. Thank you! ...
written 21 months ago by Sepd0
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Comment: C: How to filter RNAseq Data for being constant in all three biological replicates
... They are normalized. I don't know how to rely on it being deferentially expressed when there are big differences in the expression values. Sometimes it shows zero expression in two of the replicates but one of the replicates has a huge value throwing off the whole calculation. FBtr0085375 *0.091674 ...
written 21 months ago by Sepd0
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Comment: C: How to filter RNAseq Data for being constant in all three biological replicates
... Thank you. Do you know if EbSeq considers this variability too? The list I am look at are transcripts that have been marked as deferentially expressed but when looking at the expression values of the replicates you can see they are not constant. ...
written 21 months ago by Sepd0

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