User: arshil
arshil • 0
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Posts by arshil
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... thanks, yeah there was issue with the output naming. ...
written 8 months ago by
arshil • 0
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... 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"
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... import yaml
configfile: "config.yaml
SAMPLES,=glob_wildcards(config['sourcedir'] + config['datadirs']['fastq'] + "/" + "{sample}_R1.fastq.gz")
READS=["1","2"]
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... 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:
...
written 9 months ago by
arshil • 0
• updated
9 months ago by
bari.ballew • 210
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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 10 months ago by
arshil • 0
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... 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 ...
written 10 months ago by
arshil • 0
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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 10 months ago by
arshil • 0
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... 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:
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... 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. ...
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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 20 months ago by
arshil • 0
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For cut adapter using trim galore
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