Moderator: genomax2

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genomax221k
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Posts by genomax2

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Comment: C: Blast search for solanum pseudomolecules
... `pseudomolecules` refers to the DNA sequence assembly for a chromosome/genome. There is [more on this page][1]. Perhaps you should get the sequences from there. If you don't want to download locally there is an [online blast server][2] available. [1]: http://solanaceae.plantbiology.msu.edu/pgsc ...
written 5 hours ago by genomax221k
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Answer: C: Blast search for solanum pseudomolecules
... `pseudomolecules ` that is a new one for me. They seem to be available [here][1]. [1]: ftp://ftp.solgenomics.net/genomes/Solanum_tuberosum/assembly/PGSC_DM_v4.03/ ...
written 6 hours ago by genomax221k
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Comment: C: The database for GRCH 37 for rBLAST
... You could get the hg19 genome sequence from UCSC [here][1]. Uncompress and then `cat` individual chromosome files into a single large file. Create blast indexes using `makeblastdb` and then use those indexes for your program. [1]: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.ta ...
written 7 hours ago by genomax221k
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Comment: C: creating an MSA file for 20+ million reads whith non-directional sequences
... Then perhaps dedupe the dataset (`dedupe.sh` from BBMap should do it easily) before doing the MSA with that reduced dataset. ...
written 7 hours ago by genomax221k
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Comment: C: NCBI Genome Workbench cannot load sequence from BAM file provided by Veritas Gen
... You can view the VCF file in IGV as well. Use [this help page][1]. [1]: https://software.broadinstitute.org/software/igv/viewing_vcf_files ...
written 7 hours ago by genomax221k
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Comment: C: NCBI Genome Workbench cannot load sequence from BAM file provided by Veritas Gen
... The "blank" part you are referring to represents sequence that has perfectly matched the reference. You can access various display option in the right-click menu (and choose to show all bases if that is what you want). If there is a base that differs from the reference then it would be shown (like ...
written 7 hours ago by genomax221k
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Comment: C: NCBI Genome Workbench cannot load sequence from BAM file provided by Veritas Gen
... You would need to make sure that you are using the exact genome reference build that the PGP project used for generating that bam file with IGV (or any other genome browser). Unfortunately different genome builds use different nomenclature for reference genomes (e.g. chr 1 or 1 UCSC/Ensemble). The r ...
written 16 hours ago by genomax221k
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Comment: C: RNA-Seq Pathway analysis in C. elegans, Gene name conversion issues
... Closing a post is an action that is generally used by moderators to close posts that are unsuitable/unrelated to the forum. Don't use it on a question that has been answered. Since you have figured a solution out for your question go ahead and `accept` your own answer (use the check mark) to indica ...
written 17 hours ago by genomax221k
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Comment: C: NCBI Genome Workbench cannot load sequence from BAM file provided by Veritas Gen
... You should use a genome browser like [IGV][1] to view the BAM files. BAM files need to be sorted/indexed with samtools. I am not sure what OS you are using but you would need access to unix (or cygwin/virtual machine with unix on Windows) to run samtools. Edit: Were you [following this tutorial][2 ...
written 17 hours ago by genomax221k
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Comment: C: Oxford Nanopore and Illumina hybrid assembly
... If you have some time (and I think you have the resources, if I recall from a 10x thread) go ahead and give it a try. At the most the job will fail :) ...
written 20 hours ago by genomax221k

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