User: jammydodger123456

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Posts by jammydodger123456

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Cuffdiff contrast run error: "Malformed record in sample sheet" and "cuffdiff re
... Based on your suggestion, I renamed all of the bam files and moved them all into the same working directory and this has fixed it. My sample_sheet.txt now looks like this; sample_id group_label EggB1.bam Egg EggB2.bam Egg MetB1.bam Met MetB2.bam Met ...
written 3 months ago by jammydodger1234560
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Cuffdiff contrast run error: "Malformed record in sample sheet" and "cuffdiff requires at least 2 SAM files"
... I have 7 different conditions; Egg, Met, NEJ1hr, NEJ3hr, NEJ24hr, Juvenile and Adult. I want to compare Egg to all other stages individually and each stage with the one that is immediately after it ie Met-NEJ1hr, NEJ1hr-NEJ3hr etc. Following suggestions on other posts, I have tried; cuffdiff -- ...
cufflinks cuffdiff rna-seq written 3 months ago by jammydodger1234560 • updated 3 months ago by Satyajeet Khare1.1k
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Comment: C: Differences in FPKM values for same sample in multiple comparisons
... In your opinion, where there are multiple replicates for each sample, would you recommend running them all in one Tophat command prior to this, so that there is a single .bam file for each sample? If not would you advise on how the sample sheet and contrast.txt should be presented? Thanks for your c ...
written 3 months ago by jammydodger1234560
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Presenting differential expression data containing infinite log2(Fold Change)s
... I have differential expression data for my genes of interest which I would like to present in heatmaps, graphs etc. The standard value used for this seems to be the log2(FC). However, when the FPKM for genes go from 0 to x and from x to 0, this is problematic. Does anyone know how to present data co ...
rna-seq written 4 months ago by jammydodger1234560 • updated 4 months ago by Satyajeet Khare1.1k
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Answer: A: Differences in FPKM values for same sample in multiple comparisons
... Thank you Kristoffer and Satya ...
written 4 months ago by jammydodger1234560
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Comment: C: Differences in FPKM values for same sample in multiple comparisons
... It happens when I do separate commands. I'm not sure how to do those kind of comparisons in one command. Would you be able to show me the general command for that kind of comparison, or point me in the direction of any help? Thanks ...
written 4 months ago by jammydodger1234560
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Differences in FPKM values for same sample in multiple comparisons
... I have 7 samples (call them A,B,C,D,E,F,G). I want to compare all of the samples against sample A. When I run cuffdiff for A against B, A against C .... and A against G, the FPKM for gene X for sample A in the AvB comparison will be different to the FPKM value for gene X for sample A in the AvC co ...
cufflinks rna-seq written 4 months ago by jammydodger1234560
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Comment: C: Cuffdiff "No such file or directory" error
... That worked! Thank you ...
written 4 months ago by jammydodger1234560
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Comment: C: Cuffdiff "No such file or directory" error
... EggB1 is one directory within my working directory. Here's my script; #!/bin/bash #$ -N EvM #$ -o /mnt/scratch/users/40100371/Read_Files/Fhep/EggvMet.$JOB_ID # send email when job begins end or aborts #$ -M dwells01@qub.ac.uk -m bea #$ -pe smp-verbose 10 # ...
written 4 months ago by jammydodger1234560
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Cuffdiff "No such file or directory" error
... I am trying to use the job script; cuffdiff -p 10 -L Egg,Metacercaria PRJEBWB9PAULAnnotations.gff3 EggB1/tophat_out/accepted_hits.bam,EggB2/tophat_out/accepted_hits.bam MetB1/tophat_out/accepted_hits.bam,MetB2/tophat_out/accepted_hits.bam,MetB3/tophat_out/accepted_hits.bam However, I get th ...
cufflinks cuffdiff rna-seq written 4 months ago by jammydodger1234560

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