User: eidriangm

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eidriangm0
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Posts by eidriangm

<prev • 5 results • page 1 of 1 • next >
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Answer: A: from .BAM to .BAI using samtools
... bash one-liner loop: # Considering that you are inside the folder where the bams are: `for bam in $(ls *.bam); do samtools index $bam; done` ...
written 5 weeks ago by eidriangm0
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Comment: C: Patch for GEOquery package error: getGEO Error in download.file, cannot open des
... **packageVersion("GEOquery") must be >= 2.48 and maybe you have 2.40.** As it was happening to me: Probably you are just "updating" GEOquery by only calling biocLite: - source("https://bioconductor.org/biocLite.R") - biocLite("GEOquery")* However be sure that you have the latest **Biocond ...
written 11 months ago by eidriangm0
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Comment: C: How to obtain the chromosome out of an accession number?
... Well that is already given in the the question, with the Entrez ID gene 3806, which is annotated in the accession NT_113949 and I want to obtain the chromosome which is number 19. I could look for more examples but the idea is basically that, from an accession number prefixed with NT_ NW_ obtain its ...
written 14 months ago by eidriangm0
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Comment: C: How to obtain the chromosome out of an accession number?
... I saw it but all the links provided there are not working and the answer with awk + sed only applies with NC_ (already under control). Thanks anyway ...
written 14 months ago by eidriangm0
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How to obtain the chromosome out of an accession number?
... Hello Community. My problem is the following, I have some bed files whose genomic regions are annotated using the chromosome (chr__ start end ... ...), and I want to use the [ncbi gff3][1] to extract the info but this file is annotated using accession.version numbers. Bedtools oblige me to use ...
genome ncbi chromosome refseq accession written 14 months ago by eidriangm0 • updated 16 days ago by Solowars50

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