User: BioBing

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BioBing100
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Denmark
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1 month ago
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2 years, 6 months ago
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Posts by BioBing

<prev • 45 results • page 1 of 5 • next >
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Answer: A: The Biostar Handbook. A bioinformatics e-book for beginners.
... I love it! Thanks for an amazing book - and the courses in bioinformatics and python!!! When following the courses, is there a forum/thread to discuss the different lectures and topics? ...
written 13 months ago by BioBing100
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Comment: C: Cannot get efetch to download genome - what is wrong?
... This is perfect! Thank you'! ...
written 14 months ago by BioBing100
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Comment: C: Cannot get efetch to download genome - what is wrong?
... You are right! Thank you for noticing that! :) ...
written 14 months ago by BioBing100
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Answer: C: Cannot get efetch to download genome - what is wrong?
... You are right! Thanks! I think I found a way to download it using: esearch -db bioproject -query "PRJEB20069" | elink -target nuccore| efetch -format fasta > output.fa ...
written 14 months ago by BioBing100
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Cannot get efetch to download genome - what is wrong?
... Hi all, I am trying to download a genome assembly (Bioproject: PRJEB20069, assembly: GCA_900241095.1) in FASTA format using the Entrez utilities from the command line, but it continues to fail: efetch -db=nuccore -format=fasta -id=GCA_900241095.1 > output.fa I have tried varies things (us ...
genome fasta efetch entrez written 14 months ago by BioBing100 • updated 14 months ago by h.mon26k
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Contig cutoff of 300 bp - why? (Trinity transcriptome assembly)
... Hi all, This may be a stupid question, but I am curious to find out why exactly many papers chose a contig cutoff of 300 bp when performing a Trinity de novo transcriptome assembly. In my head, it makes sense since short contigs probably do not provide a lot of information and are just "contamina ...
trinity contigs rna-seq assembly written 18 months ago by BioBing100 • updated 18 months ago by jwhan.algae0
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Comment: C: DAVID gene enrichment - multiple Entrez IDs per gene symbol, what to do?
... Hi Jean-Karim, Thank you for your response! There is no reference genome available for the species I am working with, that is why I am using a Trinotate annotated gene list as background. But yes, the redundancy in the gene conversion makes it troublesome. Best, Birgitte ...
written 19 months ago by BioBing100
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DAVID gene enrichment - multiple Entrez IDs per gene symbol, what to do?
... Hi all, I need your help since I am very much in doubt about the right approach for gene enrichment analysis. For my non-model organism, I have a background list of official gene IDs (originating from a Trinotate annotated de novo transcriptome, which also assigned GO-terms to each gene) and a lis ...
gene-enrichment david go written 19 months ago by BioBing100
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Comment: C: How to split columns into rows based on gene ids in R?
... If it is not too much trouble, I would love to see an example :-) Thank you! ...
written 21 months ago by BioBing100
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Comment: C: How to split columns into rows based on gene ids in R?
... Thank you, I am new to all this "programming stuff" - learning every day :-) I tried your code, but I cannot get it to work for some reason - it returns a list of the "Gene" names without the GO_terms in the terminal, but the txt file still looks the same. But I will definitely read up on awk and ...
written 21 months ago by BioBing100

Latest awards to BioBing

Popular Question 11 months ago, created a question with more than 1,000 views. For Conflicting results with DESeq2 between versions
Popular Question 11 months ago, created a question with more than 1,000 views. For Normalization of RNAseq data and the use of de novo transcriptome
Popular Question 11 months ago, created a question with more than 1,000 views. For Kallisto/Sleuth - issue when using own annotations in the sleuth_prep() function
Popular Question 11 months ago, created a question with more than 1,000 views. For BLAST IDs into gene names? (Diamond)
Popular Question 11 months ago, created a question with more than 1,000 views. For Where to find the Trinity assembly statistics?
Popular Question 11 months ago, created a question with more than 1,000 views. For Sleuth PCA plots - how to change axis to percentage?
Popular Question 11 months ago, created a question with more than 1,000 views. For BUSCO - issue reading the fasta file
Popular Question 18 months ago, created a question with more than 1,000 views. For Trimmomatic - unknown trimmer?
Supporter 21 months ago, voted at least 25 times.

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