Reference Data¶

Preparing annotation data¶

Genome FASTA¶

Either download through Ensembl, iGenomes, or ask Globus Genomics support to build index for you.

Gene model GTF¶

Either download through Ensembl, iGenomes, or ask Globus Genomics support to build index for you.

Gene model RefFlat¶

Either download through iGenomes or build using gtf_to_refflat.sh.

Ribosomal intervals¶

Either build using generate_ribo_ints_ref.sh or in Globus Galaxy using Generate_Ribosomal_Reference_File workflow.

SNP Panel for Sample Identification¶

NGSCheckMate SNP panel (GRCh38_NGSCheckMateSNP) obtained here, based on this study

Re-mapped to GRCh38 using UCSC LiftOver tool:

GRCh37 (hg19) -> GRCh38 (hg38)

Uploaded to Globus Galaxy and added to data library as GRCh38_NGSCheckMateSNP.bed.

Non-mitochondrial BED file¶

samtools view -H lib6839_C6VG0ANXX.bam \
    | cut -f 2,3 \
    | awk '{gsub(/(SN:|LN:)/, ""); print}' \
    | egrep -v "^(K|G|M|I|V)" \
    | awk '{printf ("%s\t1\t%s\n", $1, $2)}' \
    > grch38_mitofilter.bed

samtools view -H mm9.bam | cut -f 2,3 | awk '{gsub(/(SN:|LN:)/, ""); print}' | egrep -v "^(chrM|chrUn|I|V)" | grep -v "_random" |  awk '{printf ("%s\t1\t%s\n", $1, $2)}' > mm9_mitofilter.bed

Library prep (and other) adapters¶

The main adapter reference file used for workflows is smarter_adapter_seqs_3p_5p.fasta, which includes adapter sequences for the Nextera library prep kits.

Uploading to Galaxy library¶

Create a new history or use existing ref_file_upload history.
Upload file to current history directly (Get Data -> Upload File) or using Globus transfer (Globus Data Transfer -> Get Data via Globus).
Go to the Shared Data -> Data Libraries page.
Navigate to the annotation library and the relevant subfolder for the new annotation file.
Click on the file icon with a plus sign that says “Add Datasets to Current Folder” and chose “from History”.
Select the history in which the annotation file dataset was added.
Select the file and click “Add”.