User: Ming

gravatar for Ming
Ming40
Reputation:
40
Status:
New User
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Last seen:
3 days, 10 hours ago
Joined:
11 months, 4 weeks ago
Email:
s**************@hotmail.com

Posts by Ming

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Seeking help with snakemake
... This worked for me! # rule all: Specifies the files that you would like to create during your snakemake workflow import os import snakemake.io import glob (SAMPLES,READS,) = glob_wildcards("/home/tanshiming/Downloads/{sample}_{read}_001.fastq.gz") ...
written 6 days ago by Ming40
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Comment: C: Seeking help with snakemake
... Dear WouterDeCoster, Does that mean I have to delete the rule all to run the script? ...
written 6 days ago by Ming40
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Comment: C: Seeking help with snakemake
... Dear @gb, When I try to run snakemake, this script does not seem to run: (bbmap) tanshiming@S620100019205:~/Scripts$ snakemake Building DAG of jobs... Nothing to be done. Complete log: /home/tanshiming/Scripts/.snakemake/log/2019-11-08T154720.993886.snakemake.log But I do see that ...
written 6 days ago by Ming40
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Comment: C: Seeking help with snakemake
... Thanks @gb, but I am getting the following error now: snakemake -n SyntaxError in line 22 of /home/tanshiming/Scripts/Snakefile: invalid syntax This is at the clumpify.sh line. ...
written 6 days ago by Ming40
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Seeking help with snakemake
... Dear All, I am trying to run BBMap with snakemake, and I am pretty new to this. # rule all: Specifies the files that you would like to create during your snakemake workflow import os import snakemake.io import glob (SAMPLES,READS,) = glob_wildcards("/home/tanshiming/Downlo ...
snakemake written 6 days ago by Ming40
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Comment: C: Problem with Picard MarkDuplicates
... Dear All, I have tried using the samtools version 1.9 (latest version), but I am still facing the same issue. Appreciate any help that I can get! Thank you. ...
written 24 days ago by Ming40
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Comment: C: Problem with Picard MarkDuplicates
... Dear @yztxwd, Should I just inspect the text header of the bam and the sam files? I am guessing the header should match? Will a conda-installed version of Samtools be fine? Thank you. ...
written 28 days ago by Ming40
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Comment: C: Problem with Picard MarkDuplicates
... Hello @yztxwd, How do I go about doing this? Thanks ...
written 29 days ago by Ming40
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Comment: A: Problem with Picard MarkDuplicates
... Dear All, Thanks for the reply. Below are the commands on how I got the bam file: CONTIGS=contigs.fa REF=contigs-bowtie2-reference # Build reference db bowtie2-build $CONTIGS $REF # Mapping of reads for x in *_R1_001.fastq.gz do bowtie2 -p 50 -x $REF -1 ...
written 4 weeks ago by Ming40
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Problem with Picard MarkDuplicates
... Dear All, I am trying to use the Picard MarkDuplicate tools, but came across the following error: (base) tanshiming@S620100019205:~/Downloads/sorted-bam$ java -jar /home/tanshiming/tools/picard-2.21.1/picard.jar MarkDuplicates M=1B131118A.marked_dup_metrics.txt REMOVE_DUPLICATES=true I=1B13111 ...
mapping written 4 weeks ago by Ming40 • updated 4 weeks ago by prishly10

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