User: cedrickclarido

Reputation:
20
Status:
New User
Location:
Netherlands/Rotterdam/Leiden University (Applied Science)
Last seen:
5 hours ago
Joined:
1 year ago
Email:
c*************@gmail.com

Posts by cedrickclarido

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
... Thank you the explanation sir, I tried the following and seems to get errors all the time: s1104230@Bioserver02:~/test2$ time samtools mpileup -f reference.fa aln.sorted.bam > aln2.mpileup [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 real 19m30.006s ...
written 5 hours ago by cedrickclarido20
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Comment: C: How to read VCF (v4.1) file? (student project)
... Hello, indeed the version is really old. However, as student I am limited to this version as I am working in a school's server where the tool is pre-installed. I can't seems to find any good manuals or documentations to convert pileup to bcf and bcf to vcf. As shown from my previous comment: sa ...
written 6 hours ago by cedrickclarido20
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Comment: C: How to read VCF (v4.1) file? (student project)
... Hello thank you for the link, however I did the following: samtools mpileup -f reference.fa aln.sorted.bam > aln.mpileup samtools mpileup -uf reference.fa aln.sorted.bam > calls.bcf bcftools view calls.bcf > call.vcf I am using samtools version 0.1.19. I thought mpileup sh ...
written 8 hours ago by cedrickclarido20
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How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
... Hello community, Below is a fragment of my VCF file: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aln.sorted.bam 11561 6 . C X 0 . DP=1;I16=1,0,0,0,38,1444,0,0,6,36,0,0,0,0,0,0;QS=1.000000,0.000000,0.000000,0.000000 PL 0,3,6 11561 7 . C X 0 . DP=1;I16=1,0,0,0,38,1444,0,0,6,36,0,0,1,1 ...
vcf bcf samtools variantcalling written 8 hours ago by cedrickclarido20
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Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... Hello, I tried your suggestion But I get the following error: Error in rule bowtie2Build: jobid: 0 output: index.done RuleException: CalledProcessError in line 49 of /home/s1104230/scripts/Snakefile: Command ' set -euo pipefail; bowtie2-build /home/s1104230/mapping2/referen ...
written 2 days ago by cedrickclarido20
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Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... Hello So I tried again the suggested code but it seems that the error occurs at the rev. files: MissingOutputException in line 26 of /home/s1104230/scripts/Snakefile: Missing files after 5 seconds: /home/s1104230/mapping2/reference.rev2.bt2 /home/s1104230/mapping2/reference.rev1.bt2 ...
written 2 days ago by cedrickclarido20
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Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... Hello, Using the following code: rule bowtie2Build: input: "/home/bnextgen/refgenome/infected_consensus.fasta" params: basename: "/home/s1104230/output/reference" output: output1="output/reference.1.bt2" output2="output/reference.2.bt2" ...
written 4 days ago by cedrickclarido20
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How to write the output in snakefile (snakemake) for bowtie2-build
... Hello community, I am using snakemake to make a pipeline. I want to add the bowtie2-build from bowtie2 to my current snakefile as follow: rule bowtie2Build: input: "refgenome/infected_consensus.fasta" output: "output/reference" shell: "bowtie2-build {input} {output}" So I shou ...
bowtie2 snakemake bowtie2-build snakefile written 4 days ago by cedrickclarido20 • updated 4 days ago by Eric Lim990
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How to read my Samtools mpileup?
... Hello community, I have entered the following command: time samtools mpileup -f /home/bnexta mapped.sorted.bam > variants.mpileup And If i read the head of the file, I get the following: 11567 892 t 1 ^?. G 11567 893 t 1 . G 11567 894 t 1 . G 11567 895 t 1 . G 11567 ...
samtools student mpileup written 5 days ago by cedrickclarido20 • updated 5 days ago by finswimmer6.1k
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Comment: C: Why are GC% per base important in quality control of reads?
... Yeah they look like this after quality trimming, so the lengths varies a lot. So I can assume they could be poly-A tail? ...
written 8 days ago by cedrickclarido20

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