User: BioBing

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BioBing130
Reputation:
130
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Location:
Denmark
Last seen:
1 week, 5 days ago
Joined:
3 years, 10 months ago
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b**************@live.dk

Posts by BioBing

<prev • 48 results • page 1 of 5 • next >
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Comment: C: Great Python tool(s) for simulating fake/dummy VCF files?
... Great recommendation, thanks! ...
written 14 days ago by BioBing130
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Comment: C: Great Python tool(s) for simulating fake/dummy VCF files?
... Thanks, that is a good way to approach the task! ...
written 15 days ago by BioBing130
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Great Python tool(s) for simulating fake/dummy VCF files?
... Hi all, I need to generate a large number of simulated VCF files to test (and stress test) a system. For legal reasons, the files need to be fake. Can any of you recommend a great Python tool for generating dummy VCF files? Thanks! ...
python snp written 15 days ago by BioBing130 • updated 15 days ago by genomax91k
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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 2.5 years ago by BioBing130
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Comment: C: Cannot get efetch to download genome - what is wrong?
... This is perfect! Thank you'! ...
written 2.5 years ago by BioBing130
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Comment: C: Cannot get efetch to download genome - what is wrong?
... You are right! Thank you for noticing that! :) ...
written 2.5 years ago by BioBing130
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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 2.6 years ago by BioBing130
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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 2.6 years ago by BioBing130 • updated 2.6 years ago by h.mon31k
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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 2.9 years ago by BioBing130 • updated 2.8 years ago by jwhan.algae10
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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 2.9 years ago by BioBing130

Latest awards to BioBing

Great Question 15 months ago, created a question with more than 5,000 views. For Trimmomatic - unknown trimmer?
Popular Question 15 months ago, created a question with more than 1,000 views. For Where to find the Trinity assembly statistics?
Popular Question 15 months ago, created a question with more than 1,000 views. For Trimmomatic - unknown trimmer?
Popular Question 15 months ago, created a question with more than 1,000 views. For Conflicting results with DESeq2 between versions
Popular Question 15 months ago, created a question with more than 1,000 views. For Conflicting results with DESeq2 between versions
Popular Question 15 months ago, created a question with more than 1,000 views. For DAVID gene enrichment - multiple Entrez IDs per gene symbol, what to do?
Popular Question 17 months ago, created a question with more than 1,000 views. For Conflicting results with DESeq2 between versions
Popular Question 17 months ago, created a question with more than 1,000 views. For DAVID gene enrichment - multiple Entrez IDs per gene symbol, what to do?
Popular Question 17 months ago, created a question with more than 1,000 views. For Where to find the Trinity assembly statistics?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Conflicting results with DESeq2 between versions
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Normalization of RNAseq data and the use of de novo transcriptome
Popular Question 2.3 years 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 2.3 years ago, created a question with more than 1,000 views. For BLAST IDs into gene names? (Diamond)
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Where to find the Trinity assembly statistics?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Sleuth PCA plots - how to change axis to percentage?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For BUSCO - issue reading the fasta file
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Trimmomatic - unknown trimmer?
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