User: wes

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wes20
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Posts by wes

<prev • 7 results • page 1 of 1 • next >
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How to obtain organelle genome
... I have an assembled genome derived from PacBio long read data (assembled using canu). I would like to fish out both mitochondria and chloroplast contig sequence from the assembled data. Any software recommendation? I tried to blast the assembled genome against NCBI blast but failed. There is org ...
genome written 51 minutes ago by wes20
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Comment: C: how to obtain subreads from *.bax.h5 files
... Dear Genomax I download the original format of PacBio data- three bax.h5.1 and bas.h5.1 file directly from this link under data access https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR5428623 May I know how to download as binary file? Yes, they are under the same directory (base) cbr01@cbr01-Prec ...
written 9 days ago by wes20
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how to obtain subreads from *.bax.h5 files
... I had downloaded RSII data from NCBI which consists of three *.bax.h5.1 files and one bas.h5.1 file. Next, I would like to obtain subreads file using pbh5tools. By referring to guideline below, the input is bas.h5 file but there is error. May I know if the cmd below is correct? or should I use bax ...
genome written 9 days ago by wes20 • updated 9 days ago by genomax91k
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Comment: C: Estimating Transcript Abundance with RSEM
... This is the link. https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification For bowtie2 run, the script is following the link below https://github.com/trinityrnaseq/trinityrnaseq/wiki/RNA-Seq-Read-Representation-by-Trinity-Assembly bowtie2-build Trinity.fasta Trin ...
written 19 days ago by wes20 • updated 19 days ago by i.sudbery9.4k
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Estimating Transcript Abundance with RSEM
... Dear All I would like to run Estimating Transcript Abundance for a dataset using RSEM. By referring to the link below, it mentioned if alignment_based est_method: --aln_method bowtie|bowtie2|(path to bam file) alignment method. (note: RSEM requires bowtie) ...
rna-seq written 20 days ago by wes20 • updated 19 days ago by i.sudbery9.4k
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Differential expression analysis
... Dear All I had RNAseq data from different plant tissues (eg, root, leave, fruit). I managed to perform de novo assembly using Trinity. Then, I proceed with TGICL to obtain Unigenes. In order to obtain gene expression value, I used both RSEM and salmon. Example of script for RSEM rsem-prepar ...
rna-seq written 4 weeks ago by wes20
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Problem with DESeq2 installation
... Dear All I would like to install DESeq2 for DE analysis. After I type the following script > if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") > BiocManager::install("DESeq2") The following comes out: package ‘backports’ successfully unpacked ...
R written 4 weeks ago by wes20 • updated 4 weeks ago by ATpoint40k

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