User: cpcantalapiedra

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Posts by cpcantalapiedra

<prev • 31 results • page 1 of 4 • next >
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Comment: C: How to annotate your vcf files with the GT (genotype) field
... bcf-fix.pl does not fix it? have you tried it? do you have the same mpileup result using -v? "Compute genotype likelihoods and output them in the variant call format (VCF). Output is bgzip-compressed VCF unless -u option is set." ...
written 3.0 years ago by cpcantalapiedra140
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Comment: C: How to annotate your vcf files with the GT (genotype) field
... Not sure if this paragraph could sed light: "The VCF file produced by BCFtools does not strictly conform the VCF spec. For example, the GT genotype information is not always present because for the purpose of BCF, GT is unnecessary and takes disk space. In addition, GT is not the first as is requir ...
written 3.0 years ago by cpcantalapiedra140
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Comment: C: Tools to view fastq file
... umm not sure that a tool like that exists. Maybe because just running a classic assembler for Sanger sequences or maybe Velvet, spades or ssaha should be enough. Later you could align you sequences to the assembly and watch the alignments with IGV. ...
written 3.0 years ago by cpcantalapiedra140
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Comment: C: How to annotate your vcf files with the GT (genotype) field
... Are you running the commands with BAM files from several samples or genotypes? Could you explain further or make an example of your commands? ...
written 3.0 years ago by cpcantalapiedra140
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Answer: A: Extract A Group Of Fasta Sequences From A File
... If besides an identifier you had sequence length, you could create a simple BED file and use "bedtools getfasta". An example would be: - Create a bed file from your whole fasta file. - Grep the bed lines of your identifers and pipe it to `bedtools getfasta -fi whole_fasta -bed - -fo myfasta` ...
written 3.1 years ago by cpcantalapiedra140 • updated 8 months ago by RamRS21k
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Comment: C: How to use TPM from RNA seq data analysis for differential gene expression analy
... edgeR works with raw counts, so maybe EBseq could be a better advice for TPMs? http://deweylab.biostat.wisc.edu/rsem/README.html ...
written 3.1 years ago by cpcantalapiedra140
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Answer: A: How Do I Convert Fa Files To Bed Format?
... cat $fastafile | awk '$0 ~ "^>" {name=substr($0, 2); printf name"\t1\t"} $0 !~ "^>" {printf length($0)"\t"name"\n"}' If each fasta sequence spans several lines, substitute the awk script by: BEGIN{totallen=-1;} $0 ~ "^>" {if (totallen!=-1) print totallen"\t"name; name=substr($0, 2 ...
written 3.1 years ago by cpcantalapiedra140
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Comment: C: How to assign gene names to your sequences during gene annotation?
... sed 's#Seq#ThisIsNotBlast2GO_I_promise#' ...
written 3.1 years ago by cpcantalapiedra140
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Comment: C: How do I obtain logFC values from sleuth results (both genes and isoforms)?
... uumm got no much experience with DESeq2. Contrasts can be designed in sleuth with the common GLM syntax of R within a matrix data type. For genes I got in sleuth the p and qvalues of the contrasts, so I guessed that the software had calculated somehow a beta and therefore a logFC should be available ...
written 3.1 years ago by cpcantalapiedra140
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Comment: C: How do I obtain logFC values from sleuth results (both genes and isoforms)?
... Thank you. And what about genes data? ...
written 3.1 years ago by cpcantalapiedra140

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Appreciated 3.0 years ago, created a post with more than 5 votes. For BWA MEM -T option. What does really do and how?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How do I obtain logFC values from sleuth results (both genes and isoforms)?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For What Is The Difference Between 'Samtools Index' And 'Buildbamindex' From Picard Tools
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Makeblastdb Hash_Index: What For? When To Use?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For BWA MEM -T option. What does really do and how?
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