User: marongiu.luigi

gravatar for marongiu.luigi
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Germany, Mannheim, UMM
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2 years, 10 months ago
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Posts by marongiu.luigi

<prev • 274 results • page 1 of 28 • next >
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Comment: C: GATK BaseRecalibrator No overlapping contigs found ERROR
... Good spot, it must be something with the headers in the reference. I'll try again. Thank you ...
written 2 days ago by marongiu.luigi330
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GATK BaseRecalibrator No overlapping contigs found ERROR
... 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: ...
reads gatk contigs baserecalibrator written 3 days ago by marongiu.luigi330 • updated 3 days ago by Pierre Lindenbaum113k
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Comment: C: Install vcf2bed plugin for bcftools
... 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.luigi330
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Comment: C: Install vcf2bed plugin for bcftools
... 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.luigi330
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Install vcf2bed plugin for bcftools
... 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 ...
installation vcf2bed bcftools written 10 days ago by marongiu.luigi330 • updated 10 days ago by John Marshall1.3k
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navigate IGV to the points of interest
... 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. ...
visualization mapping igv written 10 days ago by marongiu.luigi330 • updated 10 days ago by toralmanvar650
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Comment: C: Calculate CDS phase in gff3 format
... 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.luigi330
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Comment: C: convert fasta/gb to vcf
... fair enough, case closed ...
written 14 days ago by marongiu.luigi330
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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.luigi330
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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.luigi330

Latest awards to marongiu.luigi

Scholar 4 weeks ago, created an answer that has been accepted. For A: Realign BAM files to other reference file
Popular Question 5 weeks ago, created a question with more than 1,000 views. For GRCh38 toplevel fasta is empty
Supporter 9 weeks ago, voted at least 25 times.
Popular Question 3 months ago, created a question with more than 1,000 views. For GRCh38 toplevel fasta is empty
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Realign BAM files to other reference file
Popular Question 4 months ago, created a question with more than 1,000 views. For GRCh38 toplevel fasta is empty
Popular Question 5 months ago, created a question with more than 1,000 views. For GRCh38 toplevel fasta is empty
Centurion 6 months ago, created 100 posts.
Popular Question 7 months ago, created a question with more than 1,000 views. For Tophat Building transcriptome files synthax
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Popular Question 11 months ago, created a question with more than 1,000 views. For Tophat Building transcriptome files synthax
Popular Question 11 months ago, created a question with more than 1,000 views. For GRCh38 toplevel fasta is empty
Popular Question 17 months ago, created a question with more than 1,000 views. For Tophat Building transcriptome files synthax
Popular Question 17 months ago, created a question with more than 1,000 views. For FastUniq on linux terminal
Scholar 17 months ago, created an answer that has been accepted. For A: align fasta files using bowtie2
Popular Question 23 months ago, created a question with more than 1,000 views. For FastUniq on linux terminal

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