User: suzanne.mcgaugh

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United States
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4 years, 5 months ago
Joined:
6 years, 6 months ago
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In this crowd, I am prob considered a newbie- I know some basic unix, some basic python. Trying to hack through some RNAseq data.

Posts by suzanne.mcgaugh

<prev • 14 results • page 1 of 2 • next >
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Comment: C: REF, ALT not recoded after removing individual sample in VCFtools and VCFlib
... Thank you for your response. I have your code working as above. Unfortunately, this is not the solution I wanted, as it removes the invariant sites. I still want all invariant sites included in my file. VCFtools and VCFlib leave a signature of the removed sample in the ALT and REF columns, even if ...
written 4.5 years ago by suzanne.mcgaugh60
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Comment: C: REF, ALT not recoded after removing individual sample in VCFtools and VCFlib
... Thank you for your response. Things aren't quite working, I tried both with the -e commands and without. Please see below. But just to be sure to clarify, I would like to keep all sites in the file (i.e. not remove the 0/0 sites), I simply want to recode the REF, ALT, and INFO appropriately to refl ...
written 4.5 years ago by suzanne.mcgaugh60
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Comment: C: REF, ALT not recoded after removing individual sample in VCFtools and VCFlib
... Thank you for your quick response, here are my commands: java -jar /panfs/roc/groups/14/mcgaughs/mcgaughs/tools/jvarkit/dist-1.128/vcfcutsamples.jar -f /panfs/roc/scratch/mcgaugh/VCFs/Not_AA.txt -r /panfs/roc/scratch/mcgaugh/VCFs/PASS_SNP_invariant_INDELTEST2.vcf>/panfs/roc/scratch/mcgaugh/VCFs/ ...
written 4.5 years ago by suzanne.mcgaugh60
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Comment: A: REF, ALT not recoded after removing individual sample in VCFtools and VCFlib
... Thank you for your help. I am using your software and it is getting me most of the way there. Thanks!  Would you please look at these lines: I think the ref allele and INFO/FORMAT in 173 and 175 case no longer need the indication that it was deleted because those lines no longer exist in the datas ...
written 4.5 years ago by suzanne.mcgaugh60
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Job: Postdoc University of Minnesota Population Genomics Cavefish
... In collaboration with most of the US-based cavefish labs, we have generated whole genome resequencing data. The postdoctoral position would include analysis of these data and writing manuscripts. In addition, the successful candidate would gather data for some work on recombination, stress, and agi ...
genome job written 4.5 years ago by suzanne.mcgaugh60
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REF, ALT not recoded after removing individual sample in VCFtools and VCFlib
... Hi,  I have a VCF file and realized that one individual is an outlier and is often different than the others. I'd like to remove this individual and have the ALT and REF columns follow suit. For example, if only this removed individual had the ALT allele the ALT column would then have a "." in it i ...
genome next-gen alignment written 4.5 years ago by suzanne.mcgaugh60
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Answer: A: Trouble running CEGMA on the sample dataset
... Thanks! 2.4 from LPM - I just switched to 2.5 and it fixed the problem. Thanks very much! This was a big help! Suzanne ...
written 4.6 years ago by suzanne.mcgaugh60
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Answer: A: Trouble running CEGMA on the sample dataset
... Hi, I'm using ncbi_blast+/2.2.28, hmmer/3.0, geneid 1.4.4,  genewise 2.4.1, and perl 5.10.1. Everything works fine with the sample file, but I am getting the same error as above with my datafile which is a transcriptome of 46,474 ORFs. I applied the fix above, to geneid.pm and HMMstar.pm even thoug ...
written 4.6 years ago by suzanne.mcgaugh60
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bwa-0.7.12 AS:i and XS:i match but MAPQ = 0
... Hi,  I was hoping someone might be able to point me to a nice explanation of how the bwa AS:i are determined.   Also, I was hoping that someone might be able to offer an explanation for the sam alignment below. MAPQ = 0, but AS:i:90 and XS:i:90. Does this simply mean that, yes, the read mapped in ...
bwa as:i mapq written 4.7 years ago by suzanne.mcgaugh60
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Comment: C: How To Know Percentage Of Identity Between Every Pair Of Orthologous Genes In Se
... In bioedit, under 'Alignment' there is a 'Sequence Identity Matrix." Otherwise, this might be a place to start with python: http://stackoverflow.com/questions/16266622/in-python-calculate-percent-identity-between-two-strings ...
written 6.4 years ago by suzanne.mcgaugh60

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