User: T_18

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T_1820
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Posts by T_18

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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 26 days ago by T_1820
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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 26 days ago by T_1820
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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 28 days ago by T_1820
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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 9 weeks ago by T_1820 • updated 9 weeks ago by finswimmer9.8k
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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 6 months ago by T_1820
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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 6 months ago by T_1820
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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 6 months ago by T_1820
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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 6 months ago by T_1820
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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 6 months ago by T_1820 • updated 6 months ago by b.nota6.0k
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(Closed) Removing text after pattern using sed
... Dear all, I am just new in the world of sed.. Simple question, but struggling now for quit a while with this: I have a list of gene names: CYP6k1 CYP4L15 CYP354A5 CYP4d8 CYP354A5 CYP354A14 CYP4c1 CYP354A5 CYP4V2 CYP354A5 I only want to keep "CYP" and the n ...
sed unix written 6 months ago by T_1820 • updated 6 months ago by genomax62k

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Popular Question 26 days ago, created a question with more than 1,000 views. For Bulk download of gene names NCBI

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