SexFindR - Sex Chromosome Identification Pipeline

Step 1: Upload Your Data

Select your data type and upload your files

BAM Files Exactly two coordinate-sorted BAMs, same reference — Step 1 (DifCover) runs automatically

FASTQ Files Raw sequencing reads (for Step 0)

VCF Files Variant calls — runs Step 2 SNP density (VCFtools)

Click to upload or drag and drop

Supports: .bam, .fastq, .fq, .vcf, .gz (max ~40GB per file — ensure server disk/RAM)

BAM mode: Upload exactly two .bam files only (remove older BAMs if needed). They must be aligned to the same genome. If a .bai index is missing, the server creates it (may take a while). Order: files are paired in A–Z order by filename — first = male / sample1, second = female / sample2 (e.g. A_male.bam and B_female.bam; note female.bam sorts before male.bam).

Step 1.5: Sample Lists (Required for FASTQ Files)

Add your sample IDs. These must match your FASTQ file names (without _R1/_R2).

Male Sample IDs One sample ID per line. Must match FASTQ file names (e.g., if file is "sample_male_1_R1.fastq", use "sample_male_1")

Female Sample IDs One sample ID per line. Must match FASTQ file names (e.g., if file is "sample_female_1_R1.fastq", use "sample_female_1")

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Reference genome (required for FASTQ → Step 0)

Upload one reference genome file (.fna, .fa, .fasta). Bowtie2 index is built automatically inside Docker.

Reference genome file Keep exactly one reference file. If you replace it, Bowtie2 index will be rebuilt automatically.

No reference genome uploaded yet.

Step 2: Configure Parameters

This is the web form step 2 (not DifCover’s internal “stage 2”). AC is passed to DifCover for Step 1 (BAM) after mapping.

Adjustment Coefficient (AC) Accounts for differences in sequencing depth. Start with 1.0 if coverage is similar.

🧬 SexFindR

Step 1: Upload Your Data

Step 1.5: Sample Lists (Required for FASTQ Files)

Reference genome (required for FASTQ → Step 0)

Step 2: Configure Parameters

Step 3: Run Pipeline

Step 4: Results