User: anthony.nash

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Posts by anthony.nash

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Comment: C: Looking for appropriate software QC for bulk RNA seq.
... Ah, thank you. So they aren't APIs. Very sorry, I am just really rushed at the moment. I'll give them a proper look now then. ...
written 3 months ago by anthony.nash0
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Comment: C: Looking for appropriate software QC for bulk RNA seq.
... Is there anything for R? I know Fortran, Assembly, C/C++ and R. MultiQC and RSeQC look to be in python. ...
written 3 months ago by anthony.nash0
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Looking for appropriate software QC for bulk RNA seq.
... I would appreciate some assistance on a matter concerning QC of bulk RNA seq. I have a list of QC steps I ought to investigate before trying to pull out DEGs. I am in a position where I need results by yesterday; then I move onto theoretical chemistry, then pharmacology, you get the idea. Therefore ...
R qc rna-seq written 3 months ago by anthony.nash0 • updated 3 months ago by zx87546.5k
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Comment: C: Adjusting SNP frequency
... Thanks, good to know. ...
written 5 months ago by anthony.nash0
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Adjusting SNP frequency
... Hi all, I'm really looking for some help here. Again, my usual disclaimer of being neither a biologist or bioinformatician, so I apologise in advance if I mess up all of my terminologies. I am using GenomeAnalysisTK to perform SNP calling, or whatever the correct noun is which results in a VCF fil ...
snp written 5 months ago by anthony.nash0
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Comment: C: Difference in read reference names when aligning reads.
... I am afraid I don't recall where that file on my system came from. Thank you for that information, I'll try and plod on from here. ...
written 5 months ago by anthony.nash0
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Comment: C: Difference in read reference names when aligning reads.
... Ah I see! Thanks. I didn't spot a single NC notation. The file I have is hg38_GRCh38.p12.allChr.fa - any idea where to get hold of the corresponding reference file with NC rather than ref|NT/NW? I appreciate your help, I'm a little out of my skill set and comfort zone at the moment. ...
written 5 months ago by anthony.nash0
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Comment: C: Difference in read reference names when aligning reads.
... Would this be something inside the human genome *****.fa file? ...
written 5 months ago by anthony.nash0
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Difference in read reference names when aligning reads.
... This might be a newbie question, I'm a QM Chemist stepping in for a bioinformatician at work, so I am sorry in advance for the lack of necessary information required to help with my question. I have a documented number of steps to follow that allows me to align my paired-end reads to a human refer ...
genome assembly sequence written 5 months ago by anthony.nash0
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Comment: C: Pulling out the reads associated with a vcf line entry.
... Pierre, thank you for this information. I am guessing I need to go back to the person who generated the VCF file and ensure we are using the same reference file (i.e., hg38_GRCh38.p12_allChr.fa)? ...
written 5 months ago by anthony.nash0

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