User: shangyuan5000

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Posts by shangyuan5000

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Comment: C: Get a specific genotype information of RNASeq fastq files
... No. I made a blastdb from the fasta files(read length 101), and then blast the -100~+100 sequence of my allele site to the blastdb, and check all hits that include the allele site to see whether my interested allele appears or not. ...
written 9 weeks ago by shangyuan500020
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Comment: C: Get a specific genotype information of RNASeq fastq files
... My current solution is quite clumsy, with the blastn result, there are hundreds of hits with pvalue at range of E-30 or lower, and I checked them by search the NT nearby the SNP sites and confirmed the Allele information. Thanks for your kind reply, and for the review of SNP calls from RNASeq. ...
written 10 weeks ago by shangyuan500020
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Answer: A: Get a specific genotype information of RNASeq fastq files
... I tried the method by natasha.sernova: https://www.biostars.org/p/185456/#185473 It works for my question. ...
written 10 weeks ago by shangyuan500020
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Comment: C: Get a specific genotype information of RNASeq fastq files
... Thanks for the kind reply. Actually, what I want is quite simple: my interested gene has two different genotypes (and they are even different in protein sequences in some positions!), and I want the related genotypes from my RNASeq data. I think this question should be much easier than that when you ...
written 10 weeks ago by shangyuan500020
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Get a specific genotype information of RNASeq fastq files
... Hi, I have the RNA-seq data at hand, and want to get the genotype information at a specific gene location. Is there any easy way to do this? regard, Raymond ...
rna-seq snp written 10 weeks ago by shangyuan500020
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Comment: C: Salmon: Optimal k-mer size (for indexing) for RNA-seq data alignment using refer
... An update to my data: I tried kmers setting to 13,17 and 19, respectively. For 13, only 5.6% mapping rate; For k=17, ~49% mapping rate; for k=19, ~35% mapping rate. I also tried to exclude ncRNA in the mapping, by setting k=17, the mapping rate did not change much, still ~49%. Note that, for both ...
written 6 months ago by shangyuan500020
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Comment: C: Salmon: Optimal k-mer size (for indexing) for RNA-seq data alignment using refer
... I have exactly the same question, short read length(=36) and very low mapping rates (~9.5%). I used cDNA to generate my index file and run salmon in quasi-mapping mode. For the low mapping rates, there were suggestions that I should include rRNA and build the index file from gtf file.(https://ww ...
written 6 months ago by shangyuan500020
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Comment: C: Signaling in PC3 and PC4
... Thanks, Kevin. My PC1 and PC2 does not separate the samples by groups, and I have no idea what they are separating since all samples were coming from the same batch as I was told. I will follow your example first and see what's coming out. To look into the loadings seems to be a really good idea. T ...
written 9 months ago by shangyuan500020
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Signaling in PC3 and PC4
... Hi, I have for group conditions and I run PCA analysis in DESeq2. After trying different PCs in the PCA plot, I found that PC3 and PC4 plot could well separate my samples: https://ibb.co/d5mpHn ![PCA analysis PC3 and PC4][1] [1]: https://ibb.co/d5mpHn I think that means my signaling probably ...
rna-seq written 9 months ago by shangyuan500020 • updated 9 months ago by Kevin Blighe33k

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