User: colindaven

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colindaven390
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Posts by colindaven

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Answer: A: My run over-clustered - what does this mean for the data?
... Try aligning it and checking the % alignments and visualization. It's probably still pretty decent but I guess there could be a lot of duplicates.You can exclude these bioinformatically depending on the application. ...
written 7 days ago by colindaven390
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Answer: A: Faster (perhaps random) access to BAM files (for collecting statistics like aver
... sambamba depth is parallelized and quicker, set it to check 1mbp etc windows. That will be quick. Otherwise one of the picard tools might help. ...
written 7 days ago by colindaven390
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Answer: A: Annotate SNPs called from Trinity transcriptome assembly using annotations from
... Nope, can't be done as far as I know. If you have a reference genome you can map reads to that and call against that. Otherwise, you could insert the SNPs into the ref transcriptome - tools are available, like "seqtk mutfa". Then use biopython etc to translate your mutated transcripts into protei ...
written 7 days ago by colindaven390
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Comment: C: finding variants in the low to no coverage areas of bacterial genomes
... I would do an assembly - SPADES - then annotate roughly -prokka- then compare the nucleotide or aa sequences of the annotations - proteinortho. You can also look at deleted genes in the two genomes by either manually scanning or using bedtools bamcoverage and filtering for 0 coverage regions. Miss ...
written 20 days ago by colindaven390
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Comment: C: Suggestion on contig assembler which respect a single copy mutation in a nonaplo
... cov 38 is potentially useful, 11 not so much. I would expect many fragmented assemblies even if just haploid/diploid. This data is not sufficient for your goals. If you are interested in one region can't you generate a whole range of PCR products and or preferably BACS and sequence those with a lon ...
written 22 days ago by colindaven390
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Comment: C: How to extend BAC sequences with Pacbio reads in order to rebuild a genomic regi
... So here is the other alternative https://github.com/yechengxi/DBG2OLC ...
written 23 days ago by colindaven390
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Comment: C: Suggestion on contig assembler which respect a single copy mutation in a nonaplo
... Which dataset ? Pacbio or Illumina ? Coverage ? If Illumina I would say this is impossible. Assemblers are not really up to the task of generating diploid assemblies yet, with a few exceptions like Falcon-unzip ...
written 23 days ago by colindaven390
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Answer: A: workflow question - problems with gene annotation
... - if de novo use all reads - if mapping go for STAR, not bowtie2, to map splice sites accurately - following de novo mapping to genomes using gmap is highly useful Good luck ...
written 23 days ago by colindaven390
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Comment: C: How to extend BAC sequences with Pacbio reads in order to rebuild a genomic regi
... You're right about Racon, I corrected my comment. Sounds like a good dataset. I believe SSPACE longread may be able to extend assemblies, but have never done this. Basically, if Canu and Falcon - both leading assemblers - have failed, then the main alternative would be HGAP. 2MB is big for a (mu ...
written 23 days ago by colindaven390
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Answer: A: How to generate corresponding embl file with gff and fasta file of each scaffold
... If it's a bacterium maybe put it into an annotated annotation platform ? Eg NCBIs automated analysis platform. MAKER et al. will only generate a GFF3. Actually prokka will generate an EMBL or has a conversion script: https://github.com/tseemann/prokka ...
written 28 days ago by colindaven390

Latest awards to colindaven

Scholar 2 days ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 8 weeks ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
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Scholar 9 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 11 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
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