User: David

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David60
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Posts by David

<prev • 55 results • page 1 of 6 • next >
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Comment: C: How to reduce false positive whan aligning paired-end reads ?
... Yes , that´s what i thought, working with a certain % coverage, it makes a lot of sense ?? Is there any database that list all ncbi genome lengths for bacterial ?? or should i create it myself? Agree with the title, might not be appropriate ...
written 6 weeks ago by David60
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Answer: A: How to reduce false positive whan aligning paired-end reads ?
... Yes, they both map, genomes are very close so i suspect there is no real solution ??? ...
written 6 weeks ago by David60
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Comment: C: How to reduce false positive whan aligning paired-end reads ?
... Thanks for the update kevin, It´s a 2x150bp experiment. I´ve done all the above trimming and QC on the reads prior to mapping them on the database. Thanks for the bowtie2 notes , i might consider give it a try. david ...
written 6 weeks ago by David60
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Comment: C: How to reduce false positive whan aligning paired-end reads ?
... I´m testing my pipeline with a known MOCK but the idea is to apply the same pipeline to unknown metagenomic samples so removing species from my database makes no sense. ...
written 6 weeks ago by David60
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How to reduce cross mapping alignments with paired-end reads ?
... Hi, I´m trying to align paired-end reads (illumina) coming from a metagenomics experiment to a custom database of bacterial species. I´m using bwa-mem (althought could change program if required) to align reads to my genomes. It works pretty well but i have some reads mapping to two different bac ...
genome dnaseq bwa written 6 weeks ago by David60
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Comment: C: Lowest common ancestor for taxonomy
... Thanks Brian, I´d rather have a local solution than relying on web queries. ...
written 7 weeks ago by David60
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Comment: C: Lowest common ancestor for taxonomy
... Thanks Pierre, seems you need to submit a couple of taxids for LCA. In my case I can have many taxids to submit, not just tow taxids ??? Also forgot to mention that input file is a blasttab file. ...
written 7 weeks ago by David60
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Lowest common ancestor for taxonomy
... Hello, I would like to know if there is any library out there to run a lowest common ancestor on the ncbi tree. i have annotated a set of contigs into species and would like to use LCA to recover the ancestor. I have found MEGAN but it is based on java and is not very fast. is there any tool o ...
ncbi lca taxonomy tree written 7 weeks ago by David60 • updated 7 weeks ago by Brian Bushnell14k
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Comment: C: Extract Intergenic Sequences from GenBank File with Perl
... My guess is that the awk expression is: awk '{B=int($1);E=int($2);printf("NC_018520\t%d\t%d\n",B,E)}' ...
written 7 weeks ago by David60
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Comment: C: Extract Intergenic Sequences from GenBank File with Perl
... Pierre, Can you update the curl command, the awk expression is cut !!!! ...
written 7 weeks ago by David60

Latest awards to David

Student 5 months ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)
Student 6 months ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)

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