For security reasons, new user accounts are no longer automatically approved by YMAP.

After you submit a new user request via the "User" tab at left, I or another admin will
confirm your identity using resources outside YMAP before activating the account. We'll
then send you a short email to let you know the account has been activated.

Observations from data processed here.

Large FASTQ files occassionally get clipped during file transfer processes, both here and elsewhere. YMAP checks for the resulting damage and will continue processing.

Large BAM files can also be clipped during file transfer processes. YMAP doesn't check for this damage, but one example was seen where YMAP continued processing. It was a sorted BAM file and the result was a large portion at the end of the genome had a copy number estimate of zero. On a second attempt, the file uploaded and processed perfectly.

Sometimes, datasets will show a strong chromosome-end bias to the sequence read depth. If there is a structural rearrangement in the genome within the impacted areas, this bias in read depth can help you characterize the rearrangement. Using chromosome-end bias correction in these cases will lead to figures that are hard to interpret.

Though YMAP can perform an indel-realignment step during processing, the step is very slow and is not recommended.

User Manual: A detailed description of the user interface and tools available in YMAP.

Data and file format requirements.

The Yeast Mapping Analysis Pipeline (YMAP) is intended to simplify the processing of whole genome array and sequence datasets from yeast (or other small genome organisms) into simple to interpret figures illustrating large-scale genomic alterations.

The current version (v1.0) of the pipeline is designed to process the following types of data:

SnpCgh Microarray.
Whole genome next-generation-seq (WGseq).
Double digest restriction site associated sequencing (ddRADseq).

The input file format options for each data type are as follows :

1. SnpCgh microarray

Only works for arrays custom designed for Candida albicans SC5314 derivatives.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276171/

Tab-delimited text (*.tdt) with the following format (standard output from BlueFuse for Microarrays v3.6):
46 header rows, followed by data rows.
1st column: probe ID/name.
4th column: probe channel 1 data.
5th column: probe channel 2 data.
6th column: probe channel ratio data.
7th column: probe channel log₂ratio data.
Unused columns in each data lines should contain some text.

2. WGseq and 3. ddRADseq

Works for any species for which a reference genome is installed.

New reference genomes in FASTA (*.fasta) format can be installed.
Genomes much smaller or larger than the 16 Mbase Candida albicans may not work well. Please contact admin to discuss testing.
https://pubmed.ncbi.nlm.nih.gov/25505934/

Single-end reads as one file in raw FASTQ (*.fastq) or compressed (*.zip; *.fastq.gz) format.
Paired-end reads as two files in raw FASTQ (*.fastq) or two compressed (*.zip; *.fastq.gz) format.
Sequence Alignment/Map file in raw (*.sam) or compressed (*.bam) format.
For examination of custom-filtered data, tab-delimited text (*.tdt) with the following format can be used :
1st column: chromosome name (must match selected reference).
2nd column: chromosome bp coordinate.
3rd column: most common base-call at coordinate.
4th column: count of most common base-call at coordinate.
5th column: 2nd most common base-call at coordinate.
6th column: Count of 2nd most common base-call at coordinate.
7th column: 3rd most common base-call at coordinate.
8th column: Count of 3rd most common base-call at coordinate.
9th column: 4th most common base-call at coordinate.
10th column: Count of 4th most common base-call at coordinate.

Uploaded files named with other file types will be discarded.

*.tdt
*.fasta
*.fastq
*.fastq.zip
*.fastq.gz
*.sam
*.bam

Projects are listed with those needing data file upload first (highlighted in red), followed by those which are in-process (highlighted in yellow), and then those that are complete (highlighted in green). As projects transition from one category to the next, the color of their line will be updated. After a page refresh, position in the list will be updated.

Haplotype maps can be constructed in YMAP, starting from one heterozygous parent or two homozygous parent datasets. When starting from a single heterozygous parent, additional child datasets with large-scale homozygoses are needed to define the final map.