User: harrypotterandsbt

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Posts by harrypotterandsbt

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Is BETA suitable for plant research?
... The only one existed tool to do the RNA-seq and Chip-seq joint analysis is BETA.And I wonder if BETA can used in Plant research. Because I read the paper, it mentioned that BETA is used in mammalian genomes.Does it means that it cannot used in other species ? like plant? Any ideas? Thanks in advance ...
beta chip-seq rna-seq written 29 days ago by harrypotterandsbt10
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Answer: A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
... Thank you! colin.kern I got the the different between libarary fragment and sequence reads. But I don't understand why " these peaks will have a gap between them roughly the size of the average fragment length of your library " Are you mean that the the length of gap is 200~400bp. I thought the gap ...
written 6 weeks ago by harrypotterandsbt10
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Comment: C: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
... I understand the abscissa of fragemnt length peaks. It means shift watson streand by X base them readch the max peason correlation coefficient.But I really don't know the the meaning of fragment length peaks and read-length peaks and why it has some thing to do with the peason correlation coefficien ...
written 8 weeks ago by harrypotterandsbt10
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Why Chip-seq data cross correlation plot has fragment_lenth cross correlation peak and read-length peaks
... Hello. I am new to Chip-seq data analysis. And I meet the problem when I study the Chip-seq quality assessment.I really can't figure out the why the corss correlation plot has two peaks which are called fragment_length corss correlation peaks and read_length peaks. What's difference between fragmen ...
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Is there any other tool to analysis Target gene based on Chip-seq and RNA-seq joint analysis result
... I know there is a tool called BETA can analysis and predict target gene based on RNA-seq and ChIP-seq datasets. And I wonder there are any other tools can do similar work.I google it and I find there are little new tools to do th work. I don't know why ? Any ideals ? Welcome your valueable points! ...
joint-analysis chip-seq rna-seq written 9 weeks ago by harrypotterandsbt10
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Comment: C: How to build a bioinformatics server
... one half year means half a year , right? ...
written 9 weeks ago by harrypotterandsbt10
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Answer: A: Snakemake report error:Missing input files for rulle all
... I know the solution, add `,` at the tail of `05_ft/{nico}_gene.gtf` ...
written 3 months ago by harrypotterandsbt10
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Snakemake report error:Missing input files for rulle all
... I'm writing my RNA-seq pipeline by Snakemake.when I was writing the last part"rule fpkm" which is calculate fpkm value from bam files. I got the error: MissingInputException in line 3 of /root/s/r/snakemake/my_rnaseq_data/Snakefile: Missing input files for rule all: 05_ft/wt2_transcript ...
pipeline snakemake rna-seq written 3 months ago by harrypotterandsbt10
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Answer: A: Convert Gene IDs of Tomato Sol Database
... Hello everyone,I think find an alternate. I suggest everyone use SL3.0 and corresponding gtf file to run RNA-seq workflow then we will get the result that most genes are labeled by LOCXXXXXXX。then we can use clusterProfiler(R package) : downloading tomato orgdb from AnnotationHub(),using bitr funct ...
written 4 months ago by harrypotterandsbt10
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Comment: C: Convert Gene IDs of Tomato Sol Database
... It can't work when I input a list of SolycXXgXXXXXX , and I cannot find the Download page ...
written 5 months ago by harrypotterandsbt10

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