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K-mers using JEllyfish

counters sequence k-mers jellyfish written 4.0 years ago by itsthegodzgarbage • 10 • updated 10 months ago by student-t • 430

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Counting k-mers in a multifasta file

k-mer counting k-mers written 13 months ago by ldyer2006 • 20 • updated 13 months ago by Alex Reynolds ♦ 23k

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Problem: kmergenie has a minimum number of input of reads?

kmergenie k-mers written 3.2 years ago by Leandro de Mattos • 70

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k-mer tools - probability based models

rna-seq k-mers written 3.8 years ago by sam • 130 • updated 3.8 years ago by edrezen • 700

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Recent Replies

C: Selecting defined length fasta sequence and excluding them from a dataset by anis.geb.cu • 0
I haven't created a separate dataframe. The data are in fasta format in a fasta file. For example...
C: Better Way To Find The Annotation For Probes Of Microarray? by Kevin Blighe ♦ 19k
sina.majidian, GPL16977 is the HuGene-1_1-st (Affymetrix Human Gene 1.1 ST Array). The annotation...
A: Selecting defined length fasta sequence and excluding them from a dataset by hlfzeus • 110
You can use SEDA (http://www.sing-group.org/seda/), which has an option to filter sequences by le...
C: MAGMA Annotation error by Ram ♦ 15k
Please use the formatting bar (especially the `code` option) to present your post better. I've do...
C: Better Way To Find The Annotation For Probes Of Microarray? by sina.majidian • 0
Dear Jelena For GPL16977, I couldn't find the .annot file. Would you pleas help us? and, another...
C: Selecting defined length fasta sequence and excluding them from a dataset by jrj.healey • 4.2k
What format is your data in already? Have you created a dataframe? Please provide more informati...
C: TMB Tumor Mutation Burden by Jeremy Leipzig ♦ 17k
I think they sequence to ridiculously high median depth (500X) so they might have started to satu...
C: loading plink format (generated by vcftools) file into Haploview by nute11a • 0
Hello! I was trying to execute this command using PLINK v1.07 with this command. My file contains...
C: data comparison contained in two separate vcf files by Ram ♦ 15k
Why python? Python's not a great choice for native code to parse large files. You're better off u...
C: TMB Tumor Mutation Burden by genomax ♦ 47k
Please don't ask new questions as `answers` in existing threads. You can either create a new thre...
A: TMB Tumor Mutation Burden by sutturka • 110
I am also interested in calculating the TMB. I have the list of "PASS" somatic mutations from GAT...
C: Can sciclone handle multiallelic variants? by genomax ♦ 47k
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