User: jammydodger123456

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Posts by jammydodger123456

<prev • 10 results • page 1 of 1 • next >
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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 2 days 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 days ago by jammydodger1234560 • updated 4 days ago by Satyajeet790
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Answer: A: Differences in FPKM values for same sample in multiple comparisons
... Thank you Kristoffer and Satya ...
written 4 days 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 days 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 5 days ago by jammydodger1234560
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Comment: C: Cuffdiff "No such file or directory" error
... That worked! Thank you ...
written 7 days 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 10 days 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 11 days ago by jammydodger1234560
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Concatenate F read files & concatenate R read files in attempts for improved transcriptome?
... I have multiple read files across 7 stages of the life cycle of Fasciola hepatica (from the same study). There are replicates for most stages. My question is this; could I concatenate all of the forward reads into 1 file, concatenate all of the reverse reads into 1 file, then undertake a de novo tra ...
cufflinks rna-seq written 14 days ago by jammydodger1234560
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Tophat Error Message
... When I run a tophat job script; #!/bin/bash #$ -N TH_3hrB1 #$ -o /mnt/scratch/users/40100371/Read_Files/Mlig/3hrB1.$JOB_ID # send email when job begins end or aborts #$ -M dwells01@qub.ac.uk -m bea #$ -pe smp-verbose 10 #load tophat module environment ...
tophat rna-seq written 14 days ago by jammydodger1234560 • updated 14 days ago by andrew.j.skelton733.6k

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