User: arshil

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arshil0
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Posts by arshil

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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 8 days ago by arshil0 • updated 8 days ago by genomax68k
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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 8 days ago by arshil0 • updated 8 days ago by bari.ballew90
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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 days 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 23 days 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 29 days 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 4 weeks ago by arshil0 • updated 29 days ago by RamRS21k
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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 9 months ago by arshil0 • updated 9 months ago by h.mon25k
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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 11 months ago by arshil0
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Comment: C: problem with bowtie2 allignment
... Total of 50 gb memory and I tried using p as 6, still Getting the same error!! ...
written 11 months ago by arshil0
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Comment: A: problem with bowtie2 allignment
... Hi! So I am running this command on HPC cluster which has 32 cores!! ...
written 11 months ago by arshil0

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