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Comment: big loss after markduplication
by
reza
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Now, after deletion of duplicated reads, What is the problem if I want to use this data for the analyzes I mentioned earlier (SNP calling, …
Comment: Download all Bacteria accession list from NCBI
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GenoMax
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AFAIK `datasets` is only meant to work with genome level data. Doing
./datasets download genome taxon 2
will get you information abou…
Comment: Download all Bacteria accession list from NCBI
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GenoMax
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If you have access to `nr` blast database then use `blastdbcmd` which is part of `blast+` package.
blastdbcmd -db nr -taxids 2 -outfmt…
Comment: Download all Bacteria accession list from NCBI
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GenoMax
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A lot of records are going to be `WP*` accessions which point to multiple organisms. Something to keep in mind.
Comment: Download all Bacteria accession list from NCBI
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A related Python script that you could use (search by FASTA title):
https://www.biostars.org/p/279584/#279811
Comment: short length amino acids
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> Can anybody help me how to blast them locally ?
You can install `blast` program locally and use that. BLAST Handbook from NCBI: https://…
Comment: Precision of variant calling (INDELs)
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desouzareis.r
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Hi, yes it could. You can compare coverage between them, especially in regions where there are false positive and false negative variants r…
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Biostars does not have an `Introductions` tradition. I don't want to delete this post because it may ban your account. Please do not post t…
Comment: Meaning letters in TCGA sample barcode field
by
sumitguptabt
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Thank you so much @kevin I will look into it and update you ASAP.
BW
Sumit
Comment: Meaning letters in TCGA sample barcode field
by
Kevin Blighe
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Hi, you can search for these here: https://portal.gdc.cancer.gov/
They seem to be from Clinical Proteomic Tumor Analysis Consortium (CPTAC)
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Victoria
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I am sorry, I didn't realise that wasn't allowed, I have deleted the other post.
Comment: Meaning letters in TCGA sample barcode field
by
sumitguptabt
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@krushnach80 Thank you, dear, These samples are from: cancer types: bronchus and lung, subtype: adenomas and adenocarcinomas. The data is H…
Comment: Meaning letters in TCGA sample barcode field
by
krushnach80
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what samples are these which tissue type?
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