User: phongphak.06

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phongphak.0610
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Posts by phongphak.06

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Question: Normalization of read counts for Metagenomics data
... This is a gene abundance of an individual sample (not compared to the other samples). ...
written 8 weeks ago by phongphak.0610
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Question: Normalization of read counts for Metagenomics data
... Hi, I'm dealing with gene abundance analysis of metagenomics data (whole-genome shotgun seq). So I've done read count by using [featureCounts][1]. Anyway. I have no idea how to normalize since there are a lot of methods use for this purpose and I also have no experience in this analysis. So shou ...
genome R next-gen sequencing assembly written 8 weeks ago by phongphak.0610 • updated 8 weeks ago by colindaven370
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Comment: C: How to split forward and reverse reads from one fastq file?
... Thank you! It's a nice idea, but it's not working correctly. Anyway, I had tried this `awk '{if(NR%8 < 4) print}' file.fastq > file_R1.fastq` and it's worked, while I have no idea how to correct the another, since > 4 cannot extract the quality of reads (> 3 and > 5 are still not wor ...
written 3 months ago by phongphak.0610
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How to split forward and reverse reads from one fastq file?
... Hi, I have a metagenomic reads simulated by [Grinder][1] like this (example): @1/1 reference=NZ_CP009501.1 position=complement(1484183..1484382) description="Methanosarcina thermophila TM-1, complete genome" TAGTCAGTTCTGGCACGAATCCTGTCACACTCTACTTATTTTAAAATCCTTATTTATCACGATTTATATTTATAATTTATTAT ...
sequence next-gen sequencing written 3 months ago by phongphak.0610 • updated 3 months ago by Brian Bushnell14k
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The problem with sensitivity analysis of somatic variant caller
... Hello! I'm working on somatic variant identification from cancer samples. So, I try to simulate Illumina paired-end read with known variants by using VarSim (http://bioinform.github.io/varsim/), which this tools can simulate the human genome with both germline and somatic mutations (use ART tool a ...
next-gen sequence snp sequencing written 19 months ago by phongphak.0610 • updated 11 months ago by biostarsjic0
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PacBio CCS read denovo assembly failed
... Hello! I'm beginning to the field of bioinformatics (I'm 1st year student in bioinformatics and systems biology program) and I got uncorrected PacBio sequences from Xylaria sp. consist of 64 files are bax.h5, CCS reads, filtered_subreads and filtered_subreads_longest which I assembled by using celer ...
genome assembly next-gen alignment sequencing written 2.6 years ago by phongphak.0610 • updated 2.6 years ago by orange30

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For PacBio CCS read denovo assembly failed

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