User: marongiu.luigi
marongiu.luigi • 330
- Reputation:
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- Germany, Mannheim, UMM
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Posts by marongiu.luigi
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... Good spot, it must be something with the headers in the reference. I'll try again. Thank you ...
written 2 days ago by
marongiu.luigi • 330
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... Dear all,
I have extracted reads that did not mapped to a reference genome with
samtools view -h -f 4 .bam .bam
where the input file is sorted. Then I created the fastq files with:
bamToFastq -i .bam -fq .fq -fq2 .fq
gzip .fq
gzip .fq
This created many warning errors such as:
...
written 3 days ago by
marongiu.luigi • 330
• updated
3 days ago by
Pierre Lindenbaum ♦ 113k
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... so do I need to re-install/re-compile the whole BCFtools -- which I installed directly with `apt install` -- just to add vcf2bed? The instructions say: `put it to the plugins directory` and the only directory I have for bcftools/plugins is /usr/local/bcftools/plugins ...
written 9 days ago by
marongiu.luigi • 330
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... This looks simple and effective. I got this from the [human genome vcf][1]:
1 1014041 1014042 G/A +
1 1014121 1014122 C/T +
1 1014142 1014143 C/T +
1 1014178 1014179 C/T +
1 1014216 1014217 C/T +
1 1014227 1014228 G/A +
1 1014315 1014316 C/CG +
If it looks good, I think ...
written 9 days ago by
marongiu.luigi • 330
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... Dear all,
how can I install the plugin vcf2bed in ubuntu?
BCFtools was installed with `sudo apt-get install bedtools` and I followed the instructions [here][1] thus I copied the file `vcf2bed.c` into ` /usr/local/bcftools/plugins` and run `sudo make` but the error was `make: *** No targets specifi ...
written 10 days ago by
marongiu.luigi • 330
• updated
10 days ago by
John Marshall • 1.3k
4
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... Dear all,
would be possible to point directly IGV to the positions that contain reads? That is, how to navigate to the point(s) of interest?
I have an alignment with few (if any) reads mapped to a given genome that is several million bp in length. From IGV's manual, I see that one could
> a. ...
written 10 days ago by
marongiu.luigi • 330
• updated
10 days ago by
toralmanvar • 650
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... I got an exception! The GB file states:
CDS join(119458..120319,120411..120986,121098..121151,
121261..121323,121462..121572,121702..121887,
121986..122144,122290..123056,123263..124735)
I am using the code:
n=0
for i in $C ...
written 11 days ago by
marongiu.luigi • 330
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Comment:
C: convert fasta/gb to vcf
... fair enough, case closed ...
written 14 days ago by
marongiu.luigi • 330
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Comment:
C: convert fasta/gb to vcf
... I wanted to make a very general question, independent from the GATK implementation, that is: can I build a VCF from fasta/genbank? ...
written 15 days ago by
marongiu.luigi • 330
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Comment:
C: convert fasta/gb to vcf
... Thank you for the tip, but this looks a bit of an overkill, even because technically I am working with WGS, not RNAseq. The problem I am facing is: in order to call the variants I first need to re-align the reads to obtain a more accurate picture of the genomic variation; this step is done with the ...
written 15 days ago by
marongiu.luigi • 330
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