User: njbernstein

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njbernstein40
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3 years, 3 months ago
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Posts by njbernstein

<prev • 15 results • page 1 of 2 • next >
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Answer: A: voom variance modeling: lowess curve fitting notation wrong?
... Gordon Smyth answered my question here: https://support.bioconductor.org/p/115443/ ...
written 8 weeks ago by njbernstein40
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voom variance modeling: lowess curve fitting notation wrong?
... I'm reading the voom paper, and a piece of the notation doesn't seem right to me. [voom paper link][1] That or I don't understand the method, which is the most likely situation In the voom variance modeling section the following part: ![][2] In particular the following line doesn't make sense to ...
rna-seq voom written 8 weeks ago by njbernstein40
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Stringtie -> ballgown: What normalization should be done on FPKM values?
... Hi all, I used stringtie to quantify an rna experiment and then loaded that data into ballgown. The standard unit used by ballgown is FPKM, as such I'm wondering what between sample normalization could or should be done on this data. I'm mostly interested in more rarely occurring transcripts. Be ...
rna ballgow written 2.9 years ago by njbernstein40
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Answer: A: Minimac3 to plink using GCTA
... Answer: for chr in `seq 1 22`; do awk -v OFS='\t' '!($4="") , !($5="")' chr$chr.imputed.info > chr$chr.imputed.info.reworked sed -i 's/\t\t//' chr$chr.imputed.info.reworked awk '{t=$5; $5=$4; $4=t; print}' chr$chr.imputed.info.reworked > t && mv t chr$chr.imputed.info.reworked awk ...
written 2.9 years ago by njbernstein40
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Minimac3 to plink using GCTA
... Hi all, I'm trying to convert minimal dosages into beds using gcta. Here's my code: gcta64  --dosage-mach  chr22.imputed.dose     chr22.imputed.info  --make-bed --out chr22.fdgsdf My error is: Reading dosage data failed. Please check the format of the map file. Here's what my info file looks ...
gcta written 2.9 years ago by njbernstein40
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Merge beds of same cohorts: one from chip and one from exome data
... Hi all, I have two bed files each representing similar cohorts (a few subjects are not in the other). I'm trying to merge  the files there is a concatenation of sorts of the calls of the same subject from both cohorts without duplication (when there is duplication always relying on the chip genotyp ...
bed plink written 2.9 years ago by njbernstein40
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Comment: C: SpliceJumper installation issues. Particularly with make
... Great Thanks! ...
written 3.0 years ago by njbernstein40
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SpliceJumper installation issues. Particularly with make
...   I'm attempting to install splice jumper (http://www.biomedcentral.com/1471-2105/16/S17/S10, https://github.com/Reedwarbler/SpliceJumper) So I downloaded the zip, and unzipped it. Then ran make, but there is still no SpliceJumper (I have bamtools installed).  Here is the output from make: g++ ...
rna-seq written 3.0 years ago by njbernstein40 • updated 3.0 years ago by Jean-Karim Heriche17k
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Answer: A: From Illumina Final report to PLINK input
... I had to do this recently (https://www.biostars.org/p/164658/#164917) ​awk 'NR < 11 { next } !seen[$2]++ {print $2,$2,0,0}' final_report.txt > Plate3_final_report.fam awk 'NR < 11 { next } {print $2,$2,$1,$3,$4}' Plate3_final_report.txt > Plate3_final_report.lgen awk 'NR < 2 { ...
written 3.0 years ago by njbernstein40
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Comment: C: Recoding lgen into Ped using plink
... So I ran it with the latest build and got the same error: /labseq/tools/plink_linux_x86_64_dev/plink --lfile /labseq/analysis_results/projects/Nick_familial/qc/Plate3_final_report PLINK v1.90p 64-bit (4 Nov 2015) https://www.cog-genomics.org/plink2 (C) 2005-2015 Shaun Purcell, Chris ...
written 3.2 years ago by njbernstein40

Latest awards to njbernstein

Scholar 8 weeks ago, created an answer that has been accepted. For A: Minimac3 to plink using GCTA
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Stringtie -> ballgown: What normalization should be done on FPKM values?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Recoding lgen into Ped using plink
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Minimac3 to plink using GCTA
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Installing Joinx on Linux-x86_64
Scholar 2.9 years ago, created an answer that has been accepted. For A: Minimac3 to plink using GCTA

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