User: njbernstein
njbernstein • 10
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Posts by njbernstein
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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 19 months ago by
njbernstein • 10
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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 19 months ago by
njbernstein • 10
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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 19 months ago by
njbernstein • 10
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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 19 months ago by
njbernstein • 10
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... Great Thanks!
...
written 20 months ago by
njbernstein • 10
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549
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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 20 months ago by
njbernstein • 10
• updated
20 months ago by
Jean-Karim Heriche ♦ 13k
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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 20 months ago by
njbernstein • 10
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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 22 months ago by
njbernstein • 10
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... I''ll do that. Thanks!
...
written 22 months ago by
njbernstein • 10
0
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...
Hello all,
I'm trying to convert .lgen into ped files using plink
However, plink won't read my lgen file all the way.
I run
plink --lfile /labseq/analysis_results/projects/Nick_familial/qc/Plate3_final_report
And my error is:
PLINK v1.90b2i 64-bit (8 Sep 2014) https://www.c ...
written 22 months ago by
njbernstein • 10
• updated
16 months ago by
dr.akilalshawi • 0
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19 months ago,
created an answer that has been accepted.
For A: Minimac3 to plink using GCTA
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