User: vinayjrao
vinayjrao • 200
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Posts by vinayjrao
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... It works exactly as required. Thanks a lot :)
Please convert your comment to an answer so that I can accept it. ...
written 7 days ago by
vinayjrao • 200
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... Thanks a lot for the command, but could you please expain it? ...
written 7 days ago by
vinayjrao • 200
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... Hi,
The input file has over 700 lines, so I am just putting up the header followed by 2 lines -
>Name,Age,"City, Country",Profession
>Mitch,27,"Melbourne,Australia",Student
>John,31,"Boston,USA",Chef
The expected output is -
>Name Age "City,Country" Profession
>M ...
written 7 days ago by
vinayjrao • 200
0
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... Hi,
Thanks for your response, but I feel my question was not clear enough.
When the raw file (.csv) is used, I want to replace all commas (except for the ones in quotes) by tab. In the last part, I mentioned that I converted the csv file entirely to a tab-delimited file, and then tried to convert ...
written 7 days ago by
vinayjrao • 200
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... Hi,
I have a file with the following format -
>Name,Age,"City, Country",Profession
>Mitch,27,"Melbourne,Australia",Student
>John,31,"Boston,USA",Chef
I want to make tis a tab separated file, but while ignoring the commas contained within the quotes with the output file looking like -
...
written 7 days ago by
vinayjrao • 200
0
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150
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... Thank you once again. ...
written 6 weeks ago by
vinayjrao • 200
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... Thank you very much for your reply however, does this imply that `ApplyBQSR` is an alternate to `PrintReads` with respect to my request, or do I have to still use `PrintReads`? ...
written 6 weeks ago by
vinayjrao • 200
10
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5 follow
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... Hello everyone, I had been using GATK3.7 until last Septemeber to identify variants from human whole exome sequencing samples. However, recently, our institute has upgraded to GATK4.1. In accordance with GATK3.7, our pipeline identified variants from the `bam` file, which was then recalibrated and t ...
written 6 weeks ago by
vinayjrao • 200
• updated
6 weeks ago by
dare_devil • 1.4k
0
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... This works perfectly! I was wondering if I could modify the command in such a way that (added to the question are the last row and column) I separately pick the `Type` of variant without bothering about the `Exon` column.
I tried `sort -t $'\t' -k1,1 -k6,6gr inputFile | sort -t $'\t' -uk1,1 --merge ...
written 8 weeks ago by
vinayjrao • 200
2
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1
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... Hi,
I have a file containing a list of mutations of some genes, with the format -
>rsID Location GeneID Feature Exon
>NucleotideSubstitution AminoAcidSubstitution cDNA Type
>rs541031 ...
written 8 weeks ago by
vinayjrao • 200
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