User: amy16

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amy1620
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Posts by amy16

<prev • 71 results • page 1 of 8 • next >
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Recommended sequencing coverage for WGRS
... Hi all, What is the recommended sequencing coverage for whole genome resequencing data for SNP identification? Thanks ...
next-gen sequencing written 9 weeks ago by amy1620 • updated 9 weeks ago by h.mon14k
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minimum recommended length for transcript prediction -Stringtie
... Hi all, Can you please advise me on what is the minimum recommended length for transcript prediction? I am using PE reads and Stringtie tool to run the transcript assembly. Thanks ...
stringtie pe rna-seq written 10 weeks ago by amy1620
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Comment: C: Tools to do a linear or logistic regression of DEG
... Which package in R do you recommend that will be more suitable for this type of analysis? ...
written 12 weeks ago by amy1620
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Tools to do a linear or logistic regression of DEG
... Hi all, I have completed the DEG analysis following the new tuxedo pipeline and have ended up with a long list of genes/transcripts. I was thinking of doing a linear or logistic regression analysis on this list to get the best pick of the gene/ transcript that could be associated with the molecular ...
rna-seq deg written 12 weeks ago by amy1620 • updated 12 weeks ago by Kritika250
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RNA-seq read alignment to ref. genome-mismatch penalty
... Hi all, What is the advised the --mp MX,MN values to capture most of the splice variants present in the given transcriptome? Thanks Amritha ...
rna-seq hisat2 written 3 months ago by amy1620
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Comment: C: Phenotype data analysis for QTL validation
... Thanks for your reply. ...
written 3 months ago by amy1620
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Phenotype data analysis for QTL validation
... Hi all, While validating a QTL interval markers in a different set of genotypes (300 lines) from the RIL mapping population that had been originally used for the QTL identification study, do I have to use the same model that was used for the analysis while identifying the QTL interval? PS: The pheno ...
genetics qtlmapping validation written 3 months ago by amy1620 • updated 3 months ago by theobroma221.1k
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Understanding the gffcompare output for my dataset
... Hi all, Below is the output from gffcompare of assembled transcripts from my RNA-seq experiment with the reference genome annotation. I am concerned about the low precision values. Do I have to rerun my assembly? # Query mRNAs : 74136 in 32930 loci (63219 multi-exon transcripts) # ...
tuxedo rna-seq gffcomapre written 3 months ago by amy1620
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Comment: C: Estimating the abundance of the transcripts and genes using stringtie
... Thanks for your valuable suggestion. Very helpful for a beginner like me in this aspect to improve my understanding. ...
written 4 months ago by amy1620
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Estimating the abundance of the transcripts and genes using stringtie
... Hi, Given that the genes and isoforms present in one sample are rarely identical to those present in all other samples in a given experiment, and so they need to be assembled in a consistent manner so that they can be compared, so we merge these GTF files into one single file. When merging is it adv ...
stringtie rna-seq written 4 months ago by amy1620 • updated 4 months ago by Devon Ryan79k

Latest awards to amy16

Popular Question 9 weeks ago, created a question with more than 1,000 views. For SAMtools installation on windows
Rising Star 4 months ago, created 50 posts within first three months of joining.
Scholar 6 months ago, created an answer that has been accepted. For A: RNA-seq read alignment

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