User: jperezboza

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jperezboza10
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Posts by jperezboza

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Are there any RNA-seq data repositories for patients who were non-responsive to
... Check TCGA and focus on recurrent data. You may only have access to already mapped data but, depending on the tumor type you are most interested on, you can find plenty of information about recurrent patients (glioma and breast cancer, for example, have quite a few inclusions) ...
written 26 days ago by jperezboza10
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Comment: C: Is there any written script to assemble multiple fastq file from accession id?
... Are you sure this _2 or _3 are indicative R2? Is it possible you are downloading different files from the same SRA experiment? ...
written 26 days ago by jperezboza10
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Comment: C: Correcting batch effect in unevenly distributed groups
... So, using LASSO, I have constructed a signature of genes that can discriminate between patients with different diseases (A,B) from healthy controls (C). This signature is "tailored" to the first, training (= batch), cohort. The goal was to validate this signature in a second cohort (C) and see if it ...
written 4 weeks ago by jperezboza10
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Comment: C: Trimming adaptors with trimmomatic
... The adaptors from illumina have different sequences depending on the version of the kit used for the library preparation. It is possible you are just trimming the wrong sequence. As they have mentioned before, check out the "overrepresented sequences" found at the bottom of the FastQC report and you ...
written 4 weeks ago by jperezboza10
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Comment: C: Correcting batch effect in unevenly distributed groups
... Hi Kevin, By not succeeding I mean that I have not been able to get anything out of this. My code did not work and because my endgoal is not doing differential expression analysis, but obtaining a "corrected" read count table and I couldn't find any way of getting this. Also, repeating the PCA anal ...
written 4 weeks ago by jperezboza10
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Answer: A: Is there a tool to identify miRNA clusters within a list of miRNAs?
... Couldn't you create a list of clusters in GSEA and then run all your data against it? Your input could be your normalized data and GSEA will enrich specific families per conditions... ...
written 5 weeks ago by jperezboza10
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Answer: A: The number of peaks in microRNA-Seq trimmed data
... I think is common protocol to discard reads for small RNA sequencing below 15-16nt, most trimmers come with an option for that (trimmommatic and cutadapt for example). Regarding your 3rd peak, that is most likely linked to piRNAs (~30nt). Where do you see more reads? In peak 1,2 or 3? If you are us ...
written 5 weeks ago by jperezboza10
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Correcting batch effect in unevenly distributed groups
... Hello you all, I have RNA sequencing data from two different runs. In the first batch I have samples from 3 groups (A,B,C) and in the second one I have samples from 3 groups (A,C,D). My PCA data shows samples clustering by group but then separated by batch (and the batch effect is much stronger tha ...
R rna-seq batch effect written 5 weeks ago by jperezboza10

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