User: FallingBabyEagle

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Posts by FallingBabyEagle

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Comment: C: How to annotate GEO data that uses GPL13112 Illumina HiSeq 2000 (Mus musculus) p
... @genomax Thank you so much. I'll give that a go. Have a great day, everyday hero. ...
written 4 months ago by FallingBabyEagle0
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Comment: C: How to annotate GEO data that uses GPL13112 Illumina HiSeq 2000 (Mus musculus) p
... ENSMUSG00000000001 4827 ENSMUSG00000000003 0 ENSMUSG00000000028 201 ENSMUSG00000000031 20 ENSMUSG00000000037 125 ENSMUSG00000000049 3 ENSMUSG00000000056 947 ENSMUSG00000000058 1167 ENSMUSG00000000078 2009 ENSMUSG00000000085 1497 ENSMUSG00000000088 2535 ...
written 4 months ago by FallingBabyEagle0 • updated 4 months ago by genomax55k
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Comment: C: How to annotate GEO data that uses GPL13112 Illumina HiSeq 2000 (Mus musculus) p
... The text files have ensembl gene ID for mouse, and gene counts. I want to know what genes they are, without having to look them up individually. I don't wanna look up 26000 rows. ...
written 4 months ago by FallingBabyEagle0
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How to annotate GEO data that uses GPL13112 Illumina HiSeq 2000 (Mus musculus) platform?
... Hello, I've downloaded some text files from GEO, and I'm hoping to annotate these. Could someone point me in the right direction? ...
gene count written 4 months ago by FallingBabyEagle0
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I want to visualize with GenVisR, do I have to use GenomeModelingTools to annotate things?
... Hello, I would love to create a **waterfall plot** of my tumor-normal pairs with GenVisR but my files are in vcf format. I tried maftools to convert, but I couldn't get it to work. Now I'm considering using Washington University's GenomicModelingSystem to get the MGI annotation format for convenie ...
genome R next-gen snp written 5 months ago by FallingBabyEagle0 • updated 5 months ago by m_two0
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Comment: C: WXS: High amount of duplications! Enormous file size difference in normal-tumor
... 47803854 + 0 in total (QC-passed reads + QC-failed reads) 20972021 + 0 duplicates 24883875 + 0 mapped (52.05%:-nan%) 47803854 + 0 paired in sequencing 23901927 + 0 read1 23901927 + 0 read2 20554832 + 0 properly paired (43.00%:-nan%) 23992038 + 0 with itself and mate mapped 891837 + 0 singlet ...
written 6 months ago by FallingBabyEagle0
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WXS: High amount of duplications! Enormous file size difference in normal-tumor pair!
... I wanna preface this by saying I'm relatively new to NGS analysis. I recently received raw data from WXS (paired end 100bp reads with 100X coverage (12Gb data) with Agilent SureSelect All Human Exon V5 kit). I noticed something's really off from the getgo. The file size between the normal and tumo ...
alignment next-gen sequence written 6 months ago by FallingBabyEagle0

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