Page Comparison

fileFormat

Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing.

individualID

Individual IDs are necessary to create the sample sheets.

specimenID

specimen IDs are necessary to interpret the analysis.

Assay

Choose between Bulk RNA Seq or Single Cell RNA Seq.

Species

The corresponding genome requires knowledge of the species.

libraryPreparationMethod

This refers to the name of the library preparation, such as KAPA Hyper PCR 3.

Platform

This refers to the name of the platform used, for example, illumina.

readPair

Specify whether the read pair is 1 or 2.

specimenPreparationMethod

Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.

tumorType

If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type.

isStranded*

This answer should be either "yes" or "no."

readPairOrientation*

Indicate the read pair orientation, such as forward or reverse.

fileFormat

Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing.

individualID

Individual IDs are necessary to create the sample sheets.

specimenID

specimen IDs are necessary to interpret the analysis.

Assay

Choose between Bulk RNA Seq or Single Cell RNA Seq.

Species

The corresponding genome requires knowledge of the species.

libraryPreparationMethod

This refers to the name of the library preparation, such as KAPA Hyper PCR 3.

Platform

This refers to the name of the platform used, for example, illumina.

readPair

Specify whether the read pair is 1 or 2.

specimenPreparationMethod

Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.

tumorType

If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type. NOTE: Files from samples lacking tumor-normal pairs will not be eligible for Somatic variant calls or for microsatellite instability processing.

isStranded*

This answer should be either "yes" or "no."

readPairOrientation*

Indicate the read pair orientation, such as forward or reverse.

Accepted file formats include "fastq", "bam", and "cram". If provided raw data are “bam” or “cram” format, only files that have not undergone any additional filtering (i.e. retains unmapped reads, have not been trimmed, etc) will be eligible for processing. Note: WES files are not eligible for variant calling if BED file is not available

Individual IDs are necessary to create the sample sheets.

specimen IDs are necessary to interpret the analysis.

Choose between Bulk RNA Seq or Single Cell RNA Seq.

The corresponding genome requires knowledge of the species.

This refers to the name of the library preparation, such as KAPA Hyper PCR 3.

This refers to the name of the platform used, for example, illumina.

Specify whether the read pair is 1 or 2.

Minimize RNA degradation with methods such as flash freezing or RNALater. FFPE is not recommended.

If the tissue is normal, indicate "not applicable." Otherwise, specify the tumor type. NOTE: Files from samples lacking tumor-normal pairs will not be eligible for Somatic variant calls or for microsatellite instability processing.

This answer should be either "yes" or "no."

Indicate the read pair orientation, such as forward or reverse.