User: arshil
arshil • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 10 hours ago
- Joined:
- 11 months, 1 week ago
- Email:
- k*********@gmail.com
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by arshil
<prev
• 11 results •
page 1 of 2 •
next >
0
votes
1
answer
154
views
1
answers
... import yaml
configfile: "config.yaml
SAMPLES,=glob_wildcards(config['sourcedir'] + config['datadirs']['fastq'] + "/" + "{sample}_R1.fastq.gz")
READS=["1","2"]
...
4
votes
1
answer
154
views
1
answer
... 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 8 days ago by
arshil • 0
• updated
8 days ago by
bari.ballew • 90
0
votes
1
answer
111
views
1
answers
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
arshil • 0
0
votes
0
answers
90
views
0
answers
... 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 23 days ago by
arshil • 0
0
votes
1
answer
160
views
1
answers
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
arshil • 0
0
votes
1
answer
172
views
1
answers
... 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:
...
0
votes
0
answers
803
views
0
answers
... 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. ...
0
votes
0
answers
628
views
0
answers
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
arshil • 0
0
votes
0
answers
628
views
0
answers
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
arshil • 0
0
votes
0
answers
628
views
0
answers
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
arshil • 0
Latest awards to arshil
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 667 users visited in the last hour