User: bioinfo

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bioinfo680
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Posts by bioinfo

<prev • 143 results • page 1 of 15 • next >
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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 6 months ago by bioinfo680
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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 6 months ago by bioinfo680
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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 14 months ago by bioinfo680
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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 18 months ago by bioinfo680
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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 19 months ago by bioinfo680 • updated 19 months ago by Istvan Albert ♦♦ 79k
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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 3.0 years ago by bioinfo680
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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 3.2 years ago by bioinfo680 • updated 3.2 years ago by Istvan Albert ♦♦ 79k
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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 3.4 years ago by bioinfo680
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Comment: C: Getting nucleotide sequences using protein accession
... Didn't work..!! Please try once more..!! ...
written 3.4 years ago by bioinfo680
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Comment: C: Getting nucleotide sequences using protein accession
... Hi Pierre I'm interested to retrieve nucleotide sequences (!!!!) using uniprot ids. So it's not a duplicate. The other question deals with retrieving protein sequences.  ...
written 3.4 years ago by bioinfo680

Latest awards to bioinfo

Popular Question 5 months ago, created a question with more than 1,000 views. For Getting nucleotide sequences using protein accession
Epic Question 10 months ago, created a question with more than 10,000 views. For Filtering Vcf File
Popular Question 10 months ago, created a question with more than 1,000 views. For Getting nucleotide sequences using protein accession
Popular Question 10 months ago, created a question with more than 1,000 views. For Fastest and memory efficient tool for 16S RNA counts
Popular Question 10 months ago, created a question with more than 1,000 views. For Downloading protein sequences for a set of chromosomes from NCBI
Popular Question 12 months ago, created a question with more than 1,000 views. For Getting nucleotide sequences using protein accession
Popular Question 15 months ago, created a question with more than 1,000 views. For Extracting References Using Pubmed Id List
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Popular Question 21 months ago, created a question with more than 1,000 views. For Searching In Biostar
Student 22 months ago, asked a question with at least 3 up-votes. For Merging/Concatenating Vcf Files
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Good Illumina Assemler
Great Question 2.4 years ago, created a question with more than 5,000 views. For Merging/Concatenating Vcf Files
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