User: Dejian

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Dejian1.2k
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Posts by Dejian

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Comment: C: Create a custom .gtf file with a list of genes
... You mentioned "a list of genes"  you are interested in analyzing. The filtering process is to single out the genes you are interested in. Unfortunately, you are studying a non-model species. If the genome is sequenced, you can see if the genome annotation is provided. If the genome is not sequenced, ...
written 2.9 years ago by Dejian1.2k
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Does htseq-count recognize soft clipping generated by STAR?
... When I apply htseq-count to bam files generated from STAR, I encounter the same error message repeatedly (see examples below). I extracted the corresponding line from bam and found that they all contained soft clipping. I thought htseq-count could correctly handle soft clipping (http://www-huber.emb ...
htseq-count alignment star rna-seq written 3.3 years ago by Dejian1.2k
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Can SNP arrays distinguish 3 different alleles at a certain position?
... I notice that people usually use two allele-specific oligonucleotide probes (ASO) on SNP arrays to distinguish two alleles for a certain SNP position. I wonder if there is a SNP array platform that can distinguish more than two alleles for a certain position (in dbSNP, there are 3 alleles for some S ...
snp written 3.4 years ago by Dejian1.2k • updated 3.4 years ago by John12k
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Comment: C: How To Choose The K Value Of Kmer In Soapdenovo?
... After assembly, you will calculate some statistics such as contig N50 N90, scaffold N50 N90, and total scaffold length. Usually, a better Kmer gives larger contig/scaffold N50/90 values. But the total scaffold length should not deviate too much from the estimated genome size (You should estimate the ...
written 4.0 years ago by Dejian1.2k
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Answer: A: Create a custom .gtf file with a list of genes
... If you are studying a well-annotated species, you can download a GTF or GFF file from Ensembl, NCBI, or UCSC. Then, you just filter the GTF/GFF file and get the lines related to your genes. That's done. You can also check the tophat website to see whether your species in on their list. If yes, you c ...
written 4.1 years ago by Dejian1.2k
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Answer: A: What type of sequence(DNA,mRNA,cDNA) is submitted to dbSNP?
... "dbSNP accepts submissions as either genomic DNA or cDNA (i.e., sequenced mRNA transcript) sequence." For more info, refer to NCBI document. ...
written 4.1 years ago by Dejian1.2k
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Answer: A: Get dbSNP ids for a gene name
... It seems this is what you want ( ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/gene_report/ ). ...
written 4.1 years ago by Dejian1.2k
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Comment: C: very poor alignment on total RNA data from exosome
... Probably this library was sequenced together with other libraries. Check the index sequence to make sure these reads are really from your sample (assuming that Nugen ovation kit 2 also uses index seq to distinguish different samples as illumina kits). I once encountered such situation that the seq c ...
written 4.1 years ago by Dejian1.2k
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Comment: C: About DESeq2 logFC and pvalue
... Thanks for making it clear. ...
written 4.1 years ago by Dejian1.2k
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About DESeq2 logFC and pvalue
... DESeq2 gives logFC values based on fitted model. We can also get the normalized counts for each sample based on the raw counts and normalization factors, thus we can calculate the logFC ourselves using normalized counts. The question is how to report the final result. I prefer the logFC+pval/FDR fro ...
deseq2 rna-seq written 4.1 years ago by Dejian1.2k • updated 3.2 years ago by Biostar ♦♦ 20

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