User: njbernstein

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njbernstein10
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Posts by njbernstein

<prev • 13 results • page 1 of 2 • next >
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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 19 months ago by njbernstein10
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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 njbernstein10
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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 19 months ago by njbernstein10
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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 19 months ago by njbernstein10
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Comment: C: SpliceJumper installation issues. Particularly with make
... Great Thanks! ...
written 20 months ago by njbernstein10
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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 20 months ago by njbernstein10 • updated 20 months ago by Jean-Karim Heriche13k
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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 20 months ago by njbernstein10
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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 22 months ago by njbernstein10
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Comment: C: Recoding lgen into Ped using plink
... I''ll do that. Thanks!   ...
written 22 months ago by njbernstein10
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Recoding lgen into Ped using plink
...   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 ...
plink illumina final report written 22 months ago by njbernstein10 • updated 16 months ago by dr.akilalshawi0

Latest awards to njbernstein

Scholar 19 months ago, created an answer that has been accepted. For A: Minimac3 to plink using GCTA

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