User: njbernstein
njbernstein • 40
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- 3 years, 3 months ago
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Posts by njbernstein
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... Gordon Smyth answered my question here: https://support.bioconductor.org/p/115443/ ...
written 8 weeks ago by
njbernstein • 40
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... 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 ...
written 8 weeks ago by
njbernstein • 40
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... 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 ...
written 2.9 years ago by
njbernstein • 40
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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
njbernstein • 40
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... 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 ...
written 2.9 years ago by
njbernstein • 40
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... 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 ...
written 2.9 years ago by
njbernstein • 40
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... Great Thanks!
...
written 3.0 years ago by
njbernstein • 40
3
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888
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...
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++ ...
written 3.0 years ago by
njbernstein • 40
• updated
3.0 years ago by
Jean-Karim Heriche ♦ 17k
2
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...
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
njbernstein • 40
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... 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
njbernstein • 40
Latest awards to njbernstein
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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