User: iraun

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iraun3.7k
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PhD candidate at University of Oslo.

There is a distinct difference between having an open mind and having a hole in your head from which your brain leaks out. J. Randi

Posts by iraun

<prev • 375 results • page 2 of 38 • next >
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Answer: A: bam-readcount : Reference_base is not the base with highest count
... In the [bam-readcount GitHub repository][1], you can clearly understand the output format: chr position reference_base depth base:count:avg_mapping_quality:avg_basequality:avg_se_mapping_quality:num_plus_strand:num_minus_strand:avg_pos_as_fraction:avg_num_mismatches_as_fraction:avg_sum_mismatch ...
written 3.2 years ago by iraun3.7k
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Answer: A: Oncotator Most Recent Version and Data Source
... `Oncotator` last version: oncotator **v1.9.1.0** Last `data source`: [here][1] [1]: https://personal.broadinstitute.org/lichtens/oncobeta/oncotator_v1_ds_April052016.tar.gz ...
written 3.3 years ago by iraun3.7k
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Comment: C: How to preprocess, normalize, decompose a VCF file before inputting to the SNPEf
... I don't get the point about what you are exactly looking for, but [bcftools][1] is always a nice option for `VCF` processing. [1]: https://samtools.github.io/bcftools/bcftools.html ...
written 3.3 years ago by iraun3.7k
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bwa.kit: run-bwamem or bwa mem
... Hi there, I have recently realised about `bwa.kit` toolkit. [BWA.KIT][1] My questions are: - What is the difference between running `bwa mem` and running `run-bwamem` ? As far as I have read in the manual, `run-bwamem` performs *bwa mem mapping* and then a *post-processing* step. Is the mapping ...
bwa written 3.3 years ago by iraun3.7k
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Comment: C: Bash- Sort a file based on a list in another file
... Glad to help :). It takes a little bit of time and learning to get used to Biostars. However there are nice post regarding the correct use of the forum, how to ask, how to reply/comment and so on...So I'd recommend you to read them if you are planing to use the forum in the future ;) ...
written 3.4 years ago by iraun3.7k
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Answer: C: Why is it absolutely necessary to filter a VCF?
... Unfiltered data... means a lower specificity. The probability of having false positives (mutations that are not true, i.e errors) is higher than in the filtered data. In an ideal and a perfect world, when you call mutations through a Variant Calling analysis, all the true variants in the output woul ...
written 3.4 years ago by iraun3.7k
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Comment: C: SNP annotation using gff3
... It's weird that you have different scaffolds names taking in to account that it is the same genome. Are you sure that the genome you have used for variant calling is the same genome that it is annotated in the gff3 file? same genome and same version? If the answer is `yes`, if you have list with `gf ...
written 3.4 years ago by iraun3.7k
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Answer: A: Grep the first match for each line of a pattern file
... This should work: grep -f pattern_file description_file | awk -F" " '!_[$1]++' The `grep` command matches common lines between two files. The `awk` command prints out only the first match. Please, change `-F` variable if your field separator in the decription file is not a white space. ...
written 3.4 years ago by iraun3.7k
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Comment: C: Grep the first match for each line of a pattern file
... It's a good practice to give an example of your expected output. This is very helpful to have the desired answer. For other hand I would recommend you to have a look to *stackoverflow* forum since I'm pretty sure that this kind of question has been already asked before. ...
written 3.4 years ago by iraun3.7k
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Comment: C: Bash- Sort a file based on a list in another file
... I have not used file2 since I didn't know which column was length column :). In that case, you can skip the first part of my command. You can just do: while read c1; do grep -w $c1 file1.txt;done ...
written 3.4 years ago by iraun3.7k

Latest awards to iraun

Appreciated 5 months ago, created a post with more than 5 votes. For C: searching reads with a certain sequence in fastq file
Appreciated 3.0 years ago, created a post with more than 5 votes. For C: searching reads with a certain sequence in fastq file
Popular Question 3.0 years ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
Appreciated 3.0 years ago, created a post with more than 5 votes. For samtools v1.3: AD, ADF and ADR fields.
Appreciated 3.0 years ago, created a post with more than 5 votes. For C: Question about gens name starting "LOC~"
Appreciated 3.0 years ago, created a post with more than 5 votes. For C: How to remove regions from a vcf file ?
Appreciated 3.0 years ago, created a post with more than 5 votes. For C: Why is it absolutely necessary to filter a VCF?
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: GT and GL fields in VCF file
Great Question 3.0 years ago, created a question with more than 5,000 views. For GATK: HaplotypeCaller gVCF and multisample
Good Question 3.0 years ago, asked a question that was upvoted at least 5 times. For samtools v1.3: AD, ADF and ADR fields.
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: Best software to assemble bacterial genomes
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For C: searching reads with a certain sequence in fastq file
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: FPKM vs raw counts vs RPKM
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For C: Question about gens name starting "LOC~"
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: FPKM vs raw counts vs RPKM
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Get completely overlapping features
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How can I know if snp is inside a protein domain?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For SGA: get the coordinates of contig scaffolding
Popular Question 3.0 years ago, created a question with more than 1,000 views. For samtools v1.3: AD, ADF and ADR fields.
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Pindel: RPL structural variation type
Popular Question 3.0 years ago, created a question with more than 1,000 views. For scaffolding denovo contigs to genome
Popular Question 3.0 years ago, created a question with more than 1,000 views. For vcf-consensus with more than one alternative alleles
Popular Question 3.0 years ago, created a question with more than 1,000 views. For check the variations incorporated to consensus fasta by vcf-consensus
Popular Question 3.0 years ago, created a question with more than 1,000 views. For bwa.kit: run-bwamem or bwa mem
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: Best software to assemble bacterial genomes

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