User: User 4014

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User 401440
Reputation:
40
Status:
New User
Location:
Sweden
Last seen:
10 hours ago
Joined:
9 years, 1 month ago
Email:
c**********@ymail.com

Posts by User 4014

<prev • 51 results • page 1 of 6 • next >
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Comment: C: EdgeR model matrix for 2 plant genotypes with 2 treatments and 2 timepoints
... Hi, Thank you very much for your help. It is very useful. I tried making a code for (A_treatment_day12 - A_control_day12) - (A_treatment_day6 - A_control_day6). Do you mind taking a look at it and let me know how to improve it please? `rawCountTable <- read.table("counts.txt", header=TRUE, s ...
written 7 days ago by User 401440
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EdgeR model matrix for 2 plant genotypes with 2 treatments and 2 timepoints
... Hi folks, I am new in field of RNA-Seq and now trying to call DEGs from 2 plant genotypes (A -heat resistant and B-heat unresistant). I have 2 treatments (control vs treatment with 3 replicates for each, except one control I have only 2 replicates) and 2 timepoints (6 days and 12 days). Basically I ...
R rna-seq written 8 days ago by User 401440 • updated 8 days ago by rpolicastro3.2k
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Comment: C: The best way to analyze RNA-seq of multiple tree species in the same genus (with
... I think I get it now. Thanks so much .. :) ...
written 8 months ago by User 401440
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Comment: C: The best way to analyze RNA-seq of multiple tree species in the same genus (with
... Thank you very much for your comment. :) Just to be sure, I should do (1) DGE analysis for each species individually, (2) combine DGEs from each species together and run Othofinder and (3) matching such DGEs with the expressions from (1). Am I correct? Also do you have any other suggestions on what ...
written 8 months ago by User 401440
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The best way to analyze RNA-seq of multiple tree species in the same genus (with and without ref-genome)
... Dear Biostars, I am working on a project to compare gene expression between four tree species A, B, C and D. They belong to the same genus, but the phylogeny suggests B and C are from the same clade. A and D are from two different clades. For species A there is a ref genome (ca. 90,000 scaffolds), ...
R rna-seq written 8 months ago by User 401440
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de novo transcriptome assembly with >400K genes. How to proceed?
... Hi folks, I have a de novo transcriptome assembly of a polyploid tree species assembled with K=31 and min length 200 bp. The assembly contains almost 400K genes, and after a reduction with CD-HIT-EST (cut-off=0.97), I have around 350K genes left. Mapping ca. 1/4 of total reads back to the assembly ...
rna-seq written 11 months ago by User 401440 • updated 11 months ago by Biostar ♦♦ 20
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Choosing a de novo assembly for DGE analysis
... Hi folks, I have two assemblies that are built from k-mer 25 and 31. I ran TrinityStats.pl and busco (eudicot_odb10) to compare them (below). In general k-mer 31 provides better stats, except complete and single buscos that is better with k-mer 25. I prefer k-mer 31, but I am not so sure. May I hav ...
assembly rna-seq written 12 months ago by User 401440 • updated 12 months ago by xonq20
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Comment: C: Problem with FASTA headers and Trinity
... Yes, I used it to add /1 and /2 flags. I have mixed RNA-Seq data, but somehow I managed to remove the flags during rRNA clean-up (with both bowtie2 and bbduk) and binning to separate mixed reads from a plant and a fungus (with STAR). Do you have a suggestion? ...
written 12 months ago by User 401440
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Comment: C: Problem with FASTA headers and Trinity
... Actually it is from NovaSeq. The original headers end at #GTGCACCAGGAATCAC, but I guess the 0:N: 00 is added by STAR and /1 is by reformat.sh. ...
written 12 months ago by User 401440
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Comment: C: Problem with FASTA headers and Trinity
... Thanks for the link! ...
written 12 months ago by User 401440

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Popular Question 5 months ago, created a question with more than 1,000 views. For How To Categorize Transcripts To Subsets Of Go Annotation
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For MiSeq - reference database for ITS
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