User: wangdp123

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wangdp123150
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Posts by wangdp123

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Primer sequences in fastq files from 16s rRNA experiment
... Thanks for this comment. Further to this question, after removing the 5'-primers for both R1 and R2 reads from fastq files and assembling the reads from fastq files together, it is seen that the primer-like sequences appear in the 5'-end and 3'-end of the merged contigs, which is because it has seq ...
written 8 weeks ago by wangdp123150
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GTF file in Ensembl database for RNA-Seq analysis
... Hi there, I am using Ensembl gtf files to carry out RNA-Seq analysis. I am interested in the expression levels of mRNA and long-noncoding RNAs in the data and I find that the gtf files contain not only mRNA and lncRNA but also a variety of non-coding RNAs such as miRNA, snoRNA, rRNA and misc_RNA. ...
gtf rna-seq written 8 weeks ago by wangdp123150 • updated 8 weeks ago by Benn6.9k
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Primer sequences in fastq files from 16s rRNA experiment
... Hi there, I am working on the analysis of 16s RNA datasets using mothur toolkit. In the fastq files, the illumina adaptor overhang sequences have been eliminated but primer sequences are still present. 1. Would you like to provide some advice on whether the primer sequences should be removed from ...
16s rrna mothur written 8 weeks ago by wangdp123150 • updated 8 weeks ago by gb790
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GATK best practice step-by-step command lines for Arabidopsis DNA-Seq data analysis
... Hi there, I am interested in using GATK best practice to call SNP/InDels for DNA-Seq samples from Arabidopsis populations. But I am struggling to find out the step-by-step command lines for such kind of analysis. Which pipeline would you command? Could you please direct me to the correct website t ...
gatk dna-seq arabidopsis written 11 weeks ago by wangdp123150 • updated 11 weeks ago by Pierre Lindenbaum121k
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How to calculate the mapping rate from BAM files generated from BWA
... Hi there, I used BWA MEM to map the paired-end reads onto a genome but it sees that BWA didn't report the mapping metrics such as mapping rate, unique mapping rate, concordant mapping rate, unmapping rate et al. Is there any way to get this kind of information? Many thanks, Tom ...
bwa written 3 months ago by wangdp123150
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Comment: C: How to collect the phastCons and phyloP data from Ensembl
... Thanks. Any idea about how to get the conservation scores for each gene or exon by making use of the single nucleotide data? I know that the bigwig files contain the conservation score for each nucleotide. Should we use the sum or mean to calculate the scores for single gene or exon? ...
written 4 months ago by wangdp123150
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Comment: C: How to collect the phastCons and phyloP data from Ensembl
... Thanks Emily. Are there any conservation scores for Ensemblgenomes database (http://ensemblgenomes.org/) such as Ensembl Fungi, Ensembl Plants, Ensembl Protists and Ensembl Metazoa? ...
written 4 months ago by wangdp123150
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How to collect the phastCons and phyloP data from Ensembl
... Hi there, Does anybody know if Ensembl/Ensemblgenomes provides the data of sequence conservation scores (e.g., phastCons, phyloP) for each nucleotide of the genomes? If so, where to download the data? Many thanks, Tom ...
ensembl phastcons phylop written 4 months ago by wangdp123150 • updated 4 months ago by Emily_Ensembl18k
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STAR+Cufflinks for RNA-Seq analysis
... Hi there, I am using STAR+cufflink combination to handle the unstranded paired-end RNA-Seq datasets. 1. I wonder if there are a set of typical parameters for both STAR and cufflink? For STAR: STAR --runThreadN 1 --runMode alignReads --genomeDir index --readFilesIn sample_r1.fq sample_r2.fq ...
cufflinks star rna-seq written 4 months ago by wangdp123150 • updated 4 months ago by Istvan Albert ♦♦ 80k
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(Closed) TruSeq3-PE primer sequence
... Dear colleague, We are using HiSeq4000 to generate the RNA-Seq reads and can you please tell me which adapter sequence (TruSeq3-PE primer) I could use to trim the paired-end reads? Moreover, it is known that "AGATCGGAAGAGC" can be used for both ends to trim the reads for typical TruSeq adaptors. I ...
adapter trimming rna-seq written 6 months ago by wangdp123150

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