User: jammydodger123456

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Posts by jammydodger123456

<prev • 18 results • page 1 of 2 • next >
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Stringtie merge generates close duplicates of original transcripts
... Hi, I am analysing a study of the parasitic flatworm *Schistosoma mansoni* that looks at different developmental stages, although I have noticed this problem occurs with the same pipeline in different species. In attempts to generate a deeper transcriptome, I have made a gtf for each biological r ...
stringtie written 20 months ago by jammydodger12345630
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Comment: C: Stringtie output gtf file only contains STRG transripts, no original annotations
... For my first run, they actually weren't (despite coming from the same source strangely). Taking annotations and the corresponding gff file (note not gff3 that was in my original command), it still only produces STRG transcripts. It is increasing the number of total transcripts from 16,356 to 21,972 ...
written 22 months ago by jammydodger12345630
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Stringtie output gtf file only contains STRG transripts, no original annotations
... Hi, I am trying to generate a more complete transcriptome using stringtie to look for more lowly expressed transcripts. I have taken 2 read files from the same study for *Opisthorchis viverrini*, aligned them (together, as if they were replicates) to the genome using STAR, converted sam to bam with ...
stringtie written 22 months ago by jammydodger12345630
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Comment: C: FPKM values all 0 from Stringtie
... Your first command suggestion worked. Thank you very much Kevin! ...
written 2.1 years ago by jammydodger12345630
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Comment: C: FPKM values all 0 from Stringtie
... Yes, the annotations and genome are from the same source. I don't understand why this hasn't worked, as I had previously analysed transcriptomic data for this species using the same genome and annotation files and this problem didn't happen before. ...
written 2.1 years ago by jammydodger12345630
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FPKM values all 0 from Stringtie
... I have analysed a few studies from the species Schistosoma mansoni using HISAT2 and Stringtie, mostly with no problems, using the genome and corresponding annotations retrieved from the same site (http://parasite.wormbase.org/Schistosoma_mansoni_prjea36577/Info/Index). I have seen people discuss thi ...
stringtie rna-seq written 2.1 years ago by jammydodger12345630
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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 2.6 years ago by jammydodger12345630
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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 2.6 years ago by jammydodger12345630 • updated 2.6 years ago by Satyajeet Khare1.5k
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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 2.6 years ago by jammydodger12345630
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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 2.6 years ago by jammydodger12345630 • updated 2.6 years ago by Satyajeet Khare1.5k

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