User: niuyw

gravatar for niuyw
niuyw30
Reputation:
30
Status:
New User
Location:
China/Beijing
Last seen:
3 weeks, 5 days ago
Joined:
2 years, 4 months ago
Email:
x*************@qq.com

Posts by niuyw

<prev • 20 results • page 1 of 2 • next >
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Comment: C: FRIP score ATAC-seq
... Got it. Thank you :) ...
written 5 weeks ago by niuyw30
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Comment: C: FRIP score ATAC-seq
... I see. Thank you very much! I processed my data as follows: step1: align reads to the genome with bowtie2 (mm10, in my case). step2: remove duplicate reads using Picard step3: remove non-unique alignment (samtools view -q 30), mitochondrial chromosome, and keep only properly mapped re ...
written 6 weeks ago by niuyw30
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Comment: C: FRIP score ATAC-seq
... Hello, I don't get your point about `bedtools intersect`. According to [ENCODE](https://www.encodeproject.org/data-standards/terms/#enrichment), FRiP means "Fraction of all mapped reads that fall into the called peak regions, i.e. usable reads in significantly enriched peaks divided by all usable re ...
written 6 weeks ago by niuyw30
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Answer: A: Any tools for predicting binding affinity between TCR and epitode?
... Hi! I found these tools by Google, but I haven't try any of them. Hope to be helpful. * [OncoPeptVAC](https://www.medgenome.com/neo-epitope-prioritization-analysis/): a robust TCR binding algorithm to prioritize neoepitope using tumor mutation (DNAseq) and gene expression (RNAseq) data. * [TCRex](h ...
written 4 months ago by niuyw30
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Comment: C: Questions about de novo genome assembly from mixed DNA samples
... Yes, I agree with you. Because I need to set a threshold to filter out contaminated contigs, I prefer to filter on the raw data now. Thank you very much~ ...
written 8 months ago by niuyw30
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Comment: C: Questions about de novo genome assembly from mixed DNA samples
... The latest version of Kraken with default parameters was used, and the assembly was generated by Canu. According to the results of Kraken, about 75% contigs were classified into archaea, bacteria, or viral. I was also a bit shocked by this. The contaminated regions accounted for about 0.65% of the t ...
written 8 months ago by niuyw30
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Comment: C: Questions about de novo genome assembly from mixed DNA samples
... I found more than 70% contigs were classified into contaminated sequences, but most of them only had a small part (several k-mers) contaminated. There would be a few sequences left if removing the whole contigs, so I want to mask the contaminated regions with 'N'. Maybe I shoud try remove contaminat ...
written 8 months ago by niuyw30
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Comment: C: Questions about de novo genome assembly from mixed DNA samples
... Thank you for your answer! It's very clear. Now I can proceed. Thank you :) I've got another question. Maybe I should open a new thread, but you may know the circumstances better. You know, because of the tiny sizes, we used the whole bodies for sequencing, so there are considerable sequence contam ...
written 8 months ago by niuyw30
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Questions about de novo genome assembly from mixed DNA samples
... Hi, Recently I'm working on a *de novo* genome assembly project. Because the animal we study is so tiny, we had to pool DNA together from multiple individuals. And we've sequenced these DNA using both PacBio and Illumina. I've assemble the PacBio long reads into contigs, and want to do scaffolding ...
mixed dna samples hybrid reads genome assembly written 8 months ago by niuyw30 • updated 8 months ago by lieven.sterck3.9k
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Comment: C: PCA tpm fpkm
... Hello vchris, Thank you for your discussions! Seeing many threads about the normalization/preprocessing, I want to put some code pieces here, and look forward to your comments and help. Comparing to DEG analysis, I care more about data preparation. library(Rsubread) library(edgeR) ...
written 11 months ago by niuyw30

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