User: T_18

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T_1840
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Posts by T_18

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Multispecies comparison of transcriptome expression data correcting using control group
... Dear all, I’m currently working on a multispecies comparison of RNAseq transcriptome data and I would like to get your input for the design of my analysis steps. I am comparing 4 species on 3 different hosts and 1 control. So in total I am comparing 16 groups with a control for each species. I am ...
multispecies comparison rna-seq dge written 9 weeks ago by T_1840
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Comment: C: Trimming sequences based on NCBI contamination screen report
... Just for clarity, this is transcriptome data (RNAseq), meaning that some of the assembled transcripts are not necessarily full assembled genes. Now I just picked out a sequence with a region hitting Pseudomonas. Fact is that the rest of the region does hit the insect's species gene. Furthermore, I ...
written 4 months ago by T_1840
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Comment: C: Trimming sequences based on NCBI contamination screen report
... I do not have a reference genome so I can never be certain about this, only very careful. My organism is an insect so if a certain region is hitting a Pseudomonas I am quit critical and I would trim this down. Also, when I ran some of these reported sequences randomly through blast I see that region ...
written 4 months ago by T_1840
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Trimming sequences based on NCBI contamination screen report
... Hi all! I am sure I am not the first person with this problem and do not want to reinvent the wheel here, therefor I would like to know if someone has a solution for the following problem: Based on the contamination report I got from the NCBI contamination screen after trying to upload my transcri ...
ncbi assembly transcriptome written 4 months ago by T_1840 • updated 6 weeks ago by hjafar0
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Trimmomatic confirmation, multiple indeces per sample?!
... Hi! I received my HiSeq Illumina RNAseq data and want to run trimmomatic to remove bad quality reads and trim adapters. I have used trimmomatic before but I am currently in doubt if I create the adapter file in a correct way given the fact that I received multiple indeces per sample, can someone pl ...
trimmomatic rnaseq trimming written 6 months ago by T_1840 • updated 6 months ago by finswimmer11k
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Comment: C: Puzzled by GOseq analyses
... Yes, it's RNAseq data. I'm currently home, but will provide the code when I'll be in the office tomorrow. Thanks so far. ...
written 10 months ago by T_1840
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Puzzled by GOseq analyses
... Dear all, I am currently trying to run a GO enrichment analysis using GOseq but I am slightly puzzled if I am doing things correctly given my (zero) output. My endgoal is to get results I can use in GOgadget. I have the following files: - Factor labels (either differently expressed or not, so two ...
R gogadget goseq written 10 months ago by T_1840
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Comment: C: Binning GO terms into broader (more usefull) GO terms
... This seems indeed exactly what I was looking for! I'm currently following the analysis steps, but I am stuck. (That is not part of this question so do not want to put that here). ...
written 10 months ago by T_1840
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Comment: A: Binning GO terms into broader (more usefull) GO terms
... Thanks for your reply. To be precise about my goal: I have a list of 2500 differentially expressed annotated transcripts with GO terms. I think it is very usefull to split these 2500 genes into smaller chunks according to 'function' based on the GO terms. These can be relatively big like, developmen ...
written 10 months ago by T_1840
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Binning GO terms into broader (more usefull) GO terms
... Dear all, For quit some hours I have been looking for a way to bin a list of GO terms into broader, more functional, (GO term groups). More specific: I have a list of 100s of GO terms with quit specific information and I want to bin/group them into useful groups like: "development" and "metabolitio ...
go written 10 months ago by T_1840 • updated 10 months ago by Benn6.9k

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Popular Question 4 months ago, created a question with more than 1,000 views. For Bulk download of gene names NCBI
Popular Question 4 months ago, created a question with more than 1,000 views. For Bulk download of gene names NCBI

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