User: vit.filippo

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vit.filippo50
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Posts by vit.filippo

<prev • 11 results • page 1 of 2 • next >
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Calculation of the genotype likelyhood from raw data
... I am working on amplicon data from an aploid genome (same length, already aligned with a miltiple alignment). Since I cannot generate a .bam file I ve to call mutations from aligned fastq through base count generation. To validate a mutation I ve to calculate genotype likelihood, but I cannot find a ...
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Calculation of the genotype likelyhood
... I am struggling with this task since I am not able to calculate the genotype likelihood from row data. In particular, i have raw counts (A:5,C:100 ..) and quality scores associated to each base called assuming that the mapping quality is the highest. I read hundreds of post, but there is no clear st ...
genotype likelihood gatk samtools written 4 days ago by vit.filippo50
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Comment: C: pysam doesn't calculate correct nucleotide quantities from .bam file
... It worked like a charm. Thanks a lot, I didn't this section. Bests ...
written 24 days ago by vit.filippo50
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pysam doesn't calculate correct nucleotide quantities from .bam file
... I am very new to pysam, but I am trying to generate a table in which are listed all the nucleotides by genomic position divided by strand with python. I am working on amplicon data, so it would be possible that pysam would mark them as duplicates (as default). By now I simply re-wrote codes from a ...
count pysam python written 24 days ago by vit.filippo50 • updated 24 days ago by dariober11k
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Comment: C: Samtools mplileup detects wrong INDEL positions
... Thank you very much for your help! ...
written 15 months ago by vit.filippo50
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Comment: C: Samtools mplileup detects wrong INDEL positions
... The command is the following: samtools mpileup -ABQ0 -f $REF -r {} -l $BED $input bam-readcount reports that the deletion is at position 27105519 (according to IGV), but samtools says that it is at position 27105518 The output of the .mpileup is the following: chr1 27105518 C ...
written 15 months ago by vit.filippo50 • updated 15 months ago by finswimmer13k
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Comment: C: Samtools mplileup detects wrong INDEL positions
... I thank you in advance for your precious hepl! I handle the .mpileup file with an already tested perl script (https://github.com/riverlee/pileup2base/blob/master/pileup2baseindel.pl ). Before parsing the .mpileup I made sure that the script worked well and everything was good exept for deletions. I ...
written 15 months ago by vit.filippo50
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Comment: C: Samtools mplileup detects wrong INDEL positions
... samtools mpileup -ABQ0 -f $REF -r {} -l $BED $input I didn't produce a .vcf, but a .tab file with counts. RIGHT output of bam-readcount chr1 27105518 C 4069 3 4065 1 0 chr1 **27105519** A 4122 4111 6 0 0 -A 4 c ...
written 15 months ago by vit.filippo50 • updated 15 months ago by finswimmer13k
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Samtools mplileup detects wrong INDEL positions
... Dear all I've a big problem with samtools mpileup since I am trying to retriving base counts and indel but fails to locate indels. More in particular, it seems that INDELs are shifted by one position (i.e. if the deletion is located at position 2, samtools gives me that is at position 1). I've tryi ...
variant calling samtools count nuceotides mpileup written 15 months ago by vit.filippo50 • updated 15 months ago by finswimmer13k
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Answer: A: How separate one column in two columns?
... library(splitstackshape) cSplit(df, 'Gene', sep=" ", type.convert=FALSE) df<-df[-c(column_name_generated_after_split),] ...
written 15 months ago by vit.filippo50 • updated 15 months ago by ATpoint40k

Latest awards to vit.filippo

Popular Question 12 months ago, created a question with more than 1,000 views. For HTSeq count versus summarizeOverlaps, mismathc of exon counts
Scholar 15 months ago, created an answer that has been accepted. For A: How separate one column in two columns?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How separate one column in two columns?

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