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This happened when I moved the directory holding all fastq files to the an external drive. Although I kept providing the absolute path to the new location of my fastq dir within the command it kept sh…
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This is regarding _Sequence Alignment/Map Format Specification_ (2022-08-22).
§ 1.3 "The header section" lists valid values for read group platforms:
> Valid values: `CAPILLARY`, `DNBSEQ` (MGI/B…
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Hi,
I tried to index a 3 million entries FASTA file.
I stopped TMAP index after 18 hours of computing because I thought it was abnormally long. (correct me if I am wrong)
By invoking gstack, TMAP se…
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As stated in the TODO section, the current sampling method falls victim to picking additional alignments when the minimum depth has already been reached at that reference index. i.e.
`if your averag…
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See here: https://github.com/mskcc/vcf2maf/issues/95
Currently if using hg19 ref fasta, it complains for the VEP cache vs fasta discrepancy
![image](https://user-images.githubusercontent.com/381…
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Hi,
I have Ion Proton data (exome sequencing) and I have no idea how to analyze them. I've analyzed exome data from other platforms using the standard GATK pipeline, but I've not found documentation …
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The bioconda-util.Recipe class cannot handle duplicate keys.
An example of a duplicated key is in the package Mira, where there is an url for linux and an url for mac:
```
package:
name: mira
…
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I'm trying to compile and install TMAP 3.0.1 in Ubuntu 17.10.
I typed the following commands:
git clone git://github.com/iontorrent/TMAP.git
cd TMAP
git submodule init
git submodule update
git…
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```
What steps will reproduce the problem?
1. bamToBed -i foo.bam -split
on the following foo.bam file
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chr9 LN:124076172
@RG ID:sample1 P…
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```
What steps will reproduce the problem?
1. bamToBed -i foo.bam -split
on the following foo.bam file
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chr9 LN:124076172
@RG ID:sample1 P…