User: JJ

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JJ410
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1 month ago
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2 years, 6 months ago
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Posts by JJ

<prev • 137 results • page 1 of 14 • next >
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Answer: A: Is there a tool for Comparing SV between different samples?
... I found this but haven't tried it out yet... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668921/pdf/f1000research-6-13552.pdf ...
written 7 weeks ago by JJ410
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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 3 months ago by JJ410
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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 3 months ago by JJ410
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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 3 months ago by JJ410
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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 3 months ago by JJ410
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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 3 months ago by JJ410
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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 3 months ago by JJ410
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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 3 months ago by JJ410 • updated 3 months ago by grant.hovhannisyan1.4k
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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 4 months ago by JJ410 • updated 4 months ago by jared.andrews071.8k
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Comment: C: How to evaluate a biomarker signature in an independent dataset
... Thank you so much for your input! ...
written 4 months ago by JJ410

Latest awards to JJ

Student 3 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
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 Is there a tool that sorts gtf files?
Popular Question 4 months ago, created a question with more than 1,000 views. For Clustering data - data transformation (log2) highly improves clustering but why?
Voter 6 months ago, voted more than 100 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 7 months ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Centurion 8 months ago, created 100 posts.
Student 9 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 9 months ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
Supporter 14 months ago, voted at least 25 times.
Teacher 14 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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