User: hpapoli

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hpapoli70
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Sweden
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Posts by hpapoli

<prev • 26 results • page 1 of 3 • next >
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Transition and transversion as a quality of SNP call set
... Hello, One of the quality checks for a SNP call set is transition/transversion ratio. By applying a series of filters, the ratio increases which is said to be an indication of a set with less false positives. Why with filtering, TS/TV ratio increases? Thanks! ...
transition snp written 8 weeks ago by hpapoli70 • updated 8 weeks ago by Santosh Anand4.0k
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Comment: C: Calculate average mapping quality at a position
... Thanks! By the way, do you know what kind of probability distribution do mapping qualities have? ...
written 9 weeks ago by hpapoli70
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Comment: C: Calculate average mapping quality at a position
... I am not concerned about the variant positions as GATK calculates average MQ for those. I need average MQ for non-variant positions. ...
written 9 weeks ago by hpapoli70
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Calculate average mapping quality at a position
... Hello, I want to filter my non-variant positions for mapping quality. I used mpileup to output the mapping qualities across all sites. To do the filtering, can I take an arithmetic mean of the mapping qualities for each read that the base belong to? For example: NW_008793873.1 13 G 2 .^S. AB ...
mapping quality mpileup written 10 weeks ago by hpapoli70 • updated 9 weeks ago by Gabriel R.2.5k
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Comment: C: TLEN sam format
... I think I see the patten. The file is sorted based on the position coordinate and there are other reads coming in between, I find their mates in the next lines as below: SRR1144953.1448091 99 NW_008793874.1 31 60 75M = 315 359 SRR1144953.21253738 ...
written 10 weeks ago by hpapoli70
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Comment: C: TLEN sam format
... This is very clear, thank you! One more question, do a given pair always come together? That is, in the example above, we have 3 pairs and for each, we have one `QNAME`. However, in the next 3 lines of the `BAM`, we have the following: SRR1144953.1448091 99 NW_008793874.1 31 60 ...
written 10 weeks ago by hpapoli70
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TLEN sam format
... Hi, My question is about TLEN field in SAM format. Here is an example of the first 9 column of BAM file. Is `TLEN (320)` calculated as follows: `(351+62) - 93 = 320`? SRR1144953.182159 117 NW_008793873.1 2 0 * = 2 0 SRR1144953.182159 ...
alignment samtools written 10 weeks ago by hpapoli70 • updated 10 weeks ago by Amitm1.6k
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mpileup mapping quality
... Hello, When using `samtools mpileup` with `-s` option, I get a 7th column with mapping quality. I realise the mapping quality in SAM format is calculated for a given read. I wonder what does a mapping quality mean for a single base position as it is the case in mpileup? Below is an example: NW ...
samtools mapq written 11 weeks ago by hpapoli70 • updated 11 weeks ago by Kevin Blighe30k
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Mapping scaffolds to chromosomes
... Hello, I have a list of species with scaffold level assemblies. There is one species in the clade with chromosome level assembly. How can I approximately map scaffolds to chromosomes for my list of species? I know about LASTZ, one way would be to align each species to the one with chromosome level ...
assembly lastz written 11 weeks ago by hpapoli70 • updated 11 weeks ago by FGV100
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scaffold to chromosome in vcf
... Hi, I've called SNPs using the scaffold level assembly however one of the chromosomes that I'm interested in now has become chromosome level, that is the order and orientation of the scaffolds are known. I can write my own scripts but I thought to ask first. Is there any tool to convert the scaffo ...
vcf written 5 months ago by hpapoli70

Latest awards to hpapoli

Popular Question 4 months ago, created a question with more than 1,000 views. For Graphic tools to depict genes along a chromosome
Popular Question 5 months ago, created a question with more than 1,000 views. For Graphic tools to depict genes along a chromosome
Great Question 2.3 years ago, created a question with more than 5,000 views. For Removing Duplicates From Rna-Seq Data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Graphic tools to depict genes along a chromosome
Popular Question 2.3 years ago, created a question with more than 1,000 views. For intersecting bed and vcf files for polyploid samples
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Varscan for SNP calling from pooled RNA seq data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Replacing SNP positions with IUPAC code in FASTA
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Merging multiple vcf files into one
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Removing Duplicates From Rna-Seq Data
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Removing Duplicates From Rna-Seq Data

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