User: bsmith030465

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bsmith030465150
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Posts by bsmith030465

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3
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Split Fastq files
... Hi, I just got some fastq files from our sequencing center. The folder names are: DXC-1-1_lane2_20180520000/ DXC-1-1_lane4_20180520000/ DXC-1-1_lane1_20180520000/ DXC-1-1_lane3_20180520000/ DXC-1-2_lane2_20180520000/ DXC-1-2_lane4_20180520000/ DXC-1-2_lane1_20180520000/ DXC-1-2_lane3_201805 ...
illumina fastq written 4 months ago by bsmith030465150
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Comment: C: scRNA-seq: Kallisto processing of bioproject data (fastq-dump)
... I got the fastq files by executing: fastq-dump --split-files --gzip SRR8611970 ...
written 6 months ago by bsmith030465150
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Comment: C: scRNA-seq: Kallisto processing of bioproject data
... gzip -dc SRR123_1.fastq.gz | head -n 4 @NB501328:163:HK2GVBGX5:2:11101:14937:1054 ACGAGCCANTGTACCTGTGATGGAAC +NB501328:163:HK2GVBGX5:2:11101:14937:1054 AAAAAEEE#EEEEEEEEEEEEEEEEE gzip -dc SRR123_2.fastq.gz | head -n 4 @NB501328:163:HK2GVBGX5:2:11101:14937:1054 TATCTA ...
written 6 months ago by bsmith030465150
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scRNA-seq: Kallisto processing of bioproject data (fastq-dump)
... Hi, I was trying to get started with scRNA seq analysis. I downloaded a test dataset from bioproject (NCBI). However, each sample is in three fastq files (e.g. SRR123_1.fastq.gz, SRR123_2.fastq.gz, SRR123_3.fastq.gz). How do I process these in Kallisto? Do I need to combine all of these files (how ...
scrna-seq bioproject fastq-dump kallisto rna-seq written 6 months ago by bsmith030465150
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Comment: C: PLINK : Error: --tdt requires a case/control phenotype.
... Ah, my mistake!! Thanks, that worked! ...
written 7 months ago by bsmith030465150
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PLINK : Error: --tdt requires a case/control phenotype.
... Hi, I was trying to run an analysis: > plink --bfile my.samples --tdt but get the following error: Error: --tdt requires a case/control phenotype. The corresponding family file seems to be okay (i.e. case/control status looks ok): MJ19 ID55 ID57 ID56 2 2 MJ19 ID56 0 0 ...
plink written 7 months ago by bsmith030465150 • updated 7 months ago by chrchang5236.7k
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PLINK - error in --make-bed
... Hi, I was trying to convert my ped file to a bed file with the command plink --file mysamples --make-bed However, I get the error: Scanning .ped file... Possibly irregular .ped line. Restarting scan, assuming multichar alleles. Error: Half-missing call in .ped file at varia ...
plink written 9 months ago by bsmith030465150 • updated 9 months ago by chrchang5236.7k
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Comment: C: PLINK: filter for indels
... Thanks for the help and explanation. That worked! Much appreciated. ...
written 11 months ago by bsmith030465150
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Comment: C: PLINK: filter for indels
... I am trying to exclude the 'range' of snps with this file format. plink --bfile myfile --exclude snp.pos.txt --range --out myfile.indels --make-bed but it says " Note: --range flag deprecated. Use e.g. '--extract range [filename]'." It also gives an error if I use: plink --bfile myfile ...
written 11 months ago by bsmith030465150
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Comment: C: PLINK: filter for indels
... Since my variants IDs weren't unique, I did some file processing to my snps output file (myfile.snps above) and got the snp ids that I want to exclude ('snp.pos.txt'): 1 10101 10101 10101 1 10493 10493 10493 1 10560 10560 10560 1 11994 11994 11994 . . and then I ran plink ...
written 11 months ago by bsmith030465150

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
Popular Question 3 months ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
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Popular Question 4 months ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
Popular Question 6 months ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
Great Question 9 months ago, created a question with more than 5,000 views. For PLINK: Convert bed,bim, fam to vcf file
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Popular Question 10 months ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
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Popular Question 23 months ago, created a question with more than 1,000 views. For PLINK: Change affection status
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Great Question 2.9 years ago, created a question with more than 5,000 views. For PLINK: merge .bed files
Popular Question 2.9 years ago, created a question with more than 1,000 views. For GRanges intersect operation
Popular Question 2.9 years ago, created a question with more than 1,000 views. For PLINK: Change affection status
Popular Question 2.9 years ago, created a question with more than 1,000 views. For PLINK: merge .bed files
Popular Question 2.9 years ago, created a question with more than 1,000 views. For biomaRt: getBM & getSequence
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