User: arshil

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arshil0
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Posts by arshil

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Comment: C: missingoutputexception, snakemake after completing 95% analysis
... thanks, yeah there was issue with the output naming. ...
written 4 months ago by arshil0
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missingoutputexception, snakemake after completing 95% analysis
... Hi, can anyone look at the code and tell whats wrong with the code. it runs and does fastqc analysis till 95 % and than show missingf output files and stops. can anyone help me out with this . from util.varsub import varsub shell.prefix("set -euo pipefail;") configfile: "config.yaml" ...
snakemake rna-seq fastqc written 4 months ago by arshil0 • updated 3 months ago by Biostar ♦♦ 20
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Comment: A: snakemake wildcard for fastq files
... import yaml configfile: "config.yaml SAMPLES,=glob_wildcards(config['sourcedir'] + config['datadirs']['fastq'] + "/" + "{sample}_R1.fastq.gz") READS=["1","2"] ...
written 6 months ago by arshil0 • updated 6 months ago by genomax75k
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snakemake wildcard for fastq files
... Hi everyone, can anyone help me out setting up the wild card for list of paired end fastq files.(SRR7058331_1.fastq.gz, SRR7058331_2.fastq.gz I am trying to access the files from config.yaml file which looks like sourcedir: /t6/h7/data/expression refdir: /AA/Reference_genomes datadirs: ...
config.yaml snakemake rna-seq written 6 months ago by arshil0 • updated 6 months ago by bari.ballew190
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Comment: C: Snakemake, config .yaml
... everything on the config file is already Tab indented. have been stuck on this past two hours ...
written 6 months ago by arshil0
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RNA Seq, annotation, RNA Class
... Hi Everyone, Can any one suggest me how to annonate the RNA by their class(lncRNA, mRNA, snoRNA) etc. i have the bam file. thanks ...
rna-seq written 6 months ago by arshil0
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Comment: C: RNA-SEQ Snakemake error
... thank you! I didn't knew about that. will certainly do it from next time ...
written 6 months ago by arshil0
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Comment: C: i am running fastqc for 10 paired end fastq files through snakemake, can you guy
... Thanks Jeremy. I did the way you suggested it. it runs and get completed within 10 sec. but there aint any output coming. my new code as per your suggestion looks like this. SAMPLES, = glob_wildcards("/scratch/mk9uc/RNA_Seq/{sample}_1.fastq.gz") READS=["1", "2"] rule fastqc_raw: ...
written 6 months ago by arshil0 • updated 6 months ago by RamRS25k
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(Closed) cut adapter using trim galore
... Hi, can anyone help me how to trim adapter for multiple fastq files using trim galore. I have like 100 files paired end which are something like "W-CA-019-2-19_S6_LAll_R1_001.fastq.gz X-CA-022-2-20_S2_LAll_R1_001.fastq.gz W-CA-019-2-19_S6_LAll_R2_001.fastq.gz X-CA-022-2-20_S2_LAll_R2_001.fastq. ...
rna-seq written 15 months ago by arshil0 • updated 15 months ago by h.mon28k
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Comment: C: problem with bowtie2 allignment
... It was already installed on cluster! All I did was module load bowtie2 And wrote my command ...
written 17 months ago by arshil0

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Popular Question 3 months ago, created a question with more than 1,000 views. For cut adapter using trim galore

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