User: JJ

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JJ370
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Posts by JJ

<prev • 136 results • page 1 of 14 • next >
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Comment: C: Genome and transcriptome analyses in yeast
... One needs known SNPs for the recalibration step. A workaround would be to take the output of the first SNP calling, recalibrate and the call SNPs again... Have you used KOBAS before? Any tipps concerning the pathway analysis? ...
written 25 days ago by JJ370
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hey, actually I haven't gotten around to continue on this project but I will pick it up in the next couple of weeks. However, as written above I've used SNPRelate, which works. Give that one a try. I would have liked a second tool to confirm it but haven't found any. Have you tried out any tools? ...
written 26 days ago by JJ370
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Genome and transcriptome analyses in yeast
... Hi all, I've been working with higher model organisms so far (mouse/human). Now I'd like to analyse non-model yeasts. I don't see an issue with using my standard analysis workflow for this organism as well: Genome analysis: bwa-mem & GATK (although I need known SNPs for GATK - is there a be ...
snp rna-seq sequencing written 26 days ago by JJ370
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Is there a tool that can identify longer insertions using genome resequencing data?
... Hi all, I am looking for a tool that can identify longer insertions using genome resequencing data (based on Illumina reads). I am searching for something that does [this][1] basically. > Initially, Illumina paired-end sequencing reads with average Phred scores ≥20 were retained, and duplica ...
genome alignment written 26 days ago by JJ370
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Best state-of-the-art tool for ab initio-based gene prediction / annotation of genome assemblies
... Hi all, I am hoping to get some recommendations for tools to perform ab initio-based gene prediction / annotation of genome assemblies in fungi. I have come across Genscan, Augustus, GlimmerHMM, GeneID and SNAP. Any recommendation which one is the best and user-friendliest tool? Thank you! ...
assembly written 4 weeks ago by JJ370
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Comment: C: How many Mio reads are recommended for RNA-sequencing experiments in yeast?
... I always try to go for more than 3 replicates. Thanks for your input. ...
written 4 weeks ago by JJ370
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How many Mio reads are recommended for RNA-sequencing experiments in yeast?
... Hi all, For human 20-30 Mio reads per sample for DE analysis is recommended what I've read - which adds up to about 8 samples per lane for Illumina HiSeq. However, what is your recommendation for yeast? It's obviously a lot smaller. Would 15 Mio reads per sample be reasonable? Any experience her ...
rna-seq written 4 weeks ago by JJ370 • updated 4 weeks ago by grant.hovhannisyan1.2k
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How can I perform DE analysis for GRO-seq data between conditions?
... Hi all, So GRO-seq is a clever method to measure nascent RNA and I have found a [nice protocol][1] to look for active enhancers. However, it also measures nascent mRNA transcription. So now I am wondering how to do a differential expression (DE) analysis for genes between conditions. Can I simpl ...
gro-seq rna-seq written 10 weeks ago by JJ370 • updated 10 weeks ago by jared.andrews071.4k
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Comment: C: How to evaluate a biomarker signature in an independent dataset
... Thank you so much for your input! ...
written 11 weeks ago by JJ370
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Comment: C: How to evaluate a biomarker signature in an independent dataset
... Thanks for the input. But applying a model build on RNA-seq data to an independent RNA-seq dataset is generally accepted? Is there anything you could suggest on how to translate such findings between data types? ...
written 11 weeks ago by JJ370

Latest awards to JJ

Student 4 weeks ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Is there a tool that sorts gtf files?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Clustering data - data transformation (log2) highly improves clustering but why?
Voter 3 months ago, voted more than 100 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 4 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Centurion 6 months ago, created 100 posts.
Student 6 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 6 months ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
Supporter 11 months ago, voted at least 25 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Help in writing NGS pipeline (or: the road from fasta to vcf)

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