User: bioinfo

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bioinfo710
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Posts by bioinfo

<prev • 145 results • page 1 of 15 • next >
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Forum: NGS Data storage solutions for small organisations or big labs
... Hi all, I’m trying to find out and compile info on how big labs (e.g. 40+ people) or small organisations who produce large amounts of NGS data manage the data storage issue. As a small organisation, we produce 10-15 TBs of HTS data every year from large genomics and metagenomics projects. We are o ...
forum ngs storage bigdata metagenomics hts written 15 days ago by bioinfo710 • updated 9 days ago by i.sudbery4.8k
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Required packages during Cygwin installation for bioinformatics work
... Hi, many of us install Cygwin in our windows machine to have the Linux like feel. In default, many packages don't get installed when we install Cygwin. And, as a consequence, many simple commands don't work. For example, wget (https://superuser.com/questions/693284/wget-command-not-working-in-cygwin ...
wget cygwin tools written 10 weeks ago by bioinfo710 • updated 9 days ago by colindaven1.4k
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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... Thanks for book Istvan. Last year, I also bought a copy of the book with 2 years free update benefits. I was wondering if you have planned for the next update? I haven't seen any content update since Sep 2017. ...
written 10 months ago by bioinfo710
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GC content in metagenomic data
... I have sequenced a few metagenomes on Illumina (DNA extracted from fish tissue). The average number of reads I got is around 40 million/sample. I have done the preliminary QC on the datasets, and I can say that the quality of the dataset is quite high (based on the FastQC report) but I see a clear G ...
assembly metagenomics written 10 months ago by bioinfo710
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Comment: C: Rainbow assembly- segmentation fault?
... Today, when I was running the Rainbow on the cluster I noticed the similar issue. I have assigned 600 GB memory still it fails ("segmentation fault"). Now I am suspecting whether Rainbow requires few TBs of RAM at "merge" step. ...
written 19 months ago by bioinfo710
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Comment: C: Counting mapped reads from a SAM file
... Shouldn't `samtools flagstat` give the same result? I just run this and see that it gives exact counts in the third row from 'flagstat' output.e.g. "919853 + 0 mapped (96.88%:-nan%)" ...
written 22 months ago by bioinfo710
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Rarefaction curve at different sequencing depths
... I have a table which contains the number of different taxa in different samples from metagenomics data. Sample seq_depth 16S counts taxa1 taxa2 taxa3 taxa4 1 55000 230 30 39 40 12 2 72000 30 ...
rarefaction metagenomics 16s qiime written 23 months ago by bioinfo710 • updated 23 months ago by Istvan Albert ♦♦ 80k
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Subsampling a taxa abundance matrix
... Hi  I have an abundance matrix for taxonomic composition from large numbers of shotgun metagenomes that had a sequence range from 5 million to 99 million. Here is the test raw abundance data of these taxa for 4 samples. Sample_ID total_sequences Escherichia Pseudomona Bacillus Salmonella Yersin ...
taxa latest subsampling written 3.4 years ago by bioinfo710
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Handling high duplication levels in fastqc report of raw illumina data from metagenomics
... I have read a few threads here asked by others about the short read duplication levels in raw data produced by sequencing platforms. I also have read Istvan's tutorial on this issue. However, I didn't find an easy striagt forward solution on "what to do then if one have high duplication levels in th ...
latest metageomics illumina fastqc written 3.5 years ago by bioinfo710 • updated 3.5 years ago by Istvan Albert ♦♦ 80k
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Is there any toxin-antitoxin system (gene/protein) database?
... Hi  I am planning to search for bacterial toxin/antitoxin systems in a set of bacterial genomes. I was wondering if there is any resource to download toxin/antitoxin genes or protein sequences from any specialised database or NCBI or pfam? I found one (http://bioinfo-mml.sjtu.edu.cn/TADB/) but it s ...
ncbi latest database toxin written 3.7 years ago by bioinfo710

Latest awards to bioinfo

Epic Question 10 weeks ago, created a question with more than 10,000 views. For Extracting Columns From Vcf File Using Vcftools/Perl
Popular Question 8 months ago, created a question with more than 1,000 views. For Getting nucleotide sequences using protein accession
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Popular Question 10 months ago, created a question with more than 1,000 views. For Getting nucleotide sequences using protein accession
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Epic Question 15 months ago, created a question with more than 10,000 views. For Filtering Vcf File
Popular Question 15 months ago, created a question with more than 1,000 views. For Fastest and memory efficient tool for 16S RNA counts
Popular Question 15 months ago, created a question with more than 1,000 views. For Downloading protein sequences for a set of chromosomes from NCBI
Popular Question 16 months ago, created a question with more than 1,000 views. For Getting nucleotide sequences using protein accession
Popular Question 20 months ago, created a question with more than 1,000 views. For Extracting References Using Pubmed Id List
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Great Question 22 months ago, created a question with more than 5,000 views. For Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Extracting References Using Pubmed Id List
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Prophet 2.7 years ago, created a post with more than 20 followers. For Filtering Vcf File
Great Question 2.7 years ago, created a question with more than 5,000 views. For Merging/Concatenating Vcf Files
Great Question 2.7 years ago, created a question with more than 5,000 views. For Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?

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