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Forum: Site Use Guidelines
meta biostars Guidelines
updated 16 days ago by 43k • written 14.6 years ago by 100k
7
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7
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1.7k
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Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 24 days ago by ★ 2.5k • written 25 days ago by • 0
5
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4
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398
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Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
7 days ago by Estevão • 0
1
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2
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378
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Forum: VCF bulk handling
bcftools SnpEff WGS VEP VCF
22 days ago by Javier • 0
4
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2
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336
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Forum: Bioinformatics: Where do I start
Sequencing
updated 23 days ago by 43k • written 23 days ago by ▴ 10
0
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0
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186
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Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation scRNA llm
17 days ago by yxwucq • 0
6 results • Page 1 of 1
Recent Votes
A: Download data from TCGA
A: Do I need to normalize level 3 TCGA data?
A: Seqlogo and Homer
A: hmmsearch vs hmmscan - e-value, speed, & output differences?
hmmsearch vs hmmscan - e-value, speed, & output differences?
Answer: Nextflow: how to get the process work dir, within the process
use firehose_get to download TCGA data
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Comment: UMI-Tools knee-method has great influence on the results of white list by Assa Yeroslaviz ★ 1.8k
I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
Comment: Microbial Signal Transduction Database by zx8754 11k
Did you try https://mib-jouline-db.asc.ohio-state.edu/#introduction ? >The database can also be accessed via the API. The same API points …
Answer: CNVKIT - unable to produce scatter and diagram pdfs by Anitha • 0
Thank you for the information.
Comment: LncRNA Nomenclature by jain72744 ▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error by ATpoint 82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ? by ATpoint 82k
Why particular question? Rmarkdown is a composite of markdown and code. You can nicely separate free text, explanation, comments etc. from…
Comment: LncRNA Nomenclature by ATpoint 82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients by gBioStar5 ▴ 10
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients by Gordon Smyth ★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
Answer: Importing a fastq file by size_t ▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors by Philipp Bayer 8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
Comment: absolute path for symbolic links in Snakefile by Jesse ▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API by GenoMax 142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length by marco.barr ▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
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