Single Cell Analysis Program - Transcriptome (SCAP-T) (USC)

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Other (137)

3polyA(first) - Number of first reads trimmed for polyA from 3' end (phv00222477.v6.p1)
3polyA(second) - Number of second reads trimmed for polyA from 3' end (phv00222478.v6.p1)
5polyT(first) - Number of first reads trimmed for polyT from 5' end (phv00222475.v6.p1)
5polyT(second) - Number of second reads trimmed for polyT from 5' end (phv00222476.v6.p1)
ADDITIONAL_SAMPLE_COMMENTS - Additional sample comments (phv00222432.v6.p1)
AmbiguousMappedExonic - Number of reads that mapped ambiguosly to exons of more than one gene and were not counted (phv00222493.v6.p1)
AmbiguousMappedIntronic - Number of reads that mapped ambiguosly to introns of more than one gene and were not counted (phv00222499.v7.p1)
ANALYTE_TYPE - Analyte type (phv00222380.v6.p1)
aRNAPrimer(first) - Number of first reads trimmed for the aRNA primer (phv00222471.v6.p1)
aRNAPrimer(second) - Number of second reads trimmed for the aRNA primer (phv00222472.v6.p1)
aRNAPrimerRC(first) - Number of first reads trimmed for the reverse complement of aRNA primer (phv00222473.v6.p1)
aRNAPrimerRC(second) - Number of second reads trimmed for the reverse complement of aRNA primer (phv00222474.v6.p1)
AvgInpReadLen - Average read length (phv00222483.v6.p1)
AvgReadPerGeneExonic - Average number of reads that are exonic per gene (phv00222490.v6.p1)
AvgReadPerGeneIntronic - Average number of reads that are intronic per gene (phv00222496.v7.p1)
AvgUniqMapLen - Average read length for uniquely mapped reads (phv00222484.v6.p1)
BARCODE - Unique sequence that is part of the Illumina barcode (phv00222426.v6.p1)
BIOPSY_COMMENTS - Any comments from the surgeon who carried out the biopsy (phv00222388.v6.p1)
BIOPSY_ID - Identifier to indicate the samples collected from the same biopsy (phv00222382.v6.p1)
BLAST_Bacteria - Number of BLAST matches to Bacteria (phv00222445.v6.p1)
BLAST_ERCC - Number of BLAST matches to ERCC (phv00222453.v6.p1)
BLAST_Fish - Number of BLAST matches to Fish (phv00222446.v6.p1)
BLAST_Fly - Number of BLAST matches to Fly (phv00222447.v6.p1)
BLAST_HitsNotCounted - Number of BLAST matches to any other species (phv00222452.v6.p1)
BLAST_HitsNotTarget_or_ERCC - Percentage hits that map neither to the Human genome nor to ERCC sequences (phv00222444.v6.p1)
BLAST_Human - Number of BLAST matches to Human (phv00222448.v6.p1)
BLAST_Mouse - Number of BLAST matches to Mouse (phv00222449.v6.p1)
BLAST_Rat - Number of BLAST matches to Rat (phv00222450.v6.p1)
BLAST_TotalHits - The number of reads out of 5000 randomly selected reads that map against the nt database using BLAST (phv00222443.v6.p1)
BLAST_version - Blast version used (phv00222440.v6.p1)
BLAST_Yeast - Number of BLAST matches to Yeast (phv00222451.v6.p1)
BODY_SITE - Body site where sample was collected (phv00222384.v6.p1)
C1_ADDITIONAL_REAGENTS_ADDED - Additional reagents added besides the standard (phv00222404.v6.p1)
C1_CHIP - C1 Chip information (phv00222403.v6.p1)
C1_EXP_ID - Unique ID to identify samples that were collected using the same C1 experiment (if applicable) (phv00222401.v6.p1)
C1_SAMPLE_LOAD - Fresh/Frozen nuclei loaded on the C1 chip (phv00222402.v6.p1)
cDNA_BY - Code for the person who prepared the cDNA (phv00222414.v6.p1)
cDNA_DATE - CDNA preparation date (phv00222415.v6.p1)
CDS_RC(first) - Number of reads trimmed for the CDS 3' Adapter Reverse complement (phv00222481.v6.p1)
CDS(first) - Number of reads trimmed for the CDS 3' Adapter (phv00222480.v6.p1)
CELL_SUBCLASS - Specifies the cell sub-class. For instance: pyramidal, 5-HT, interneuron (phv00222419.v6.p1)
DEMULTIPLEXER - Demultiplexer used (phv00222397.v6.p1)
EPHYS_ID - Unique ID for the Ephys recording (phv00222501.v6.p1)
EPHYS_PROTOCOL_FILENAME - EPhys protocol filename (phv00222505.v6.p1)
EPHYS_PROTOCOL_NAME - EPhys protocol name (phv00222504.v6.p1)
FastQC_version - FastQC version used (phv00222441.v6.p1)
FMAID - Foundational Model of Anatomy ID for the body site where the biopsy is taken from (phv00222385.v6.p1)
GencodeVersion - Gencode version (phv00222436.v6.p1)
HARVEST_METHOD - Method by which cells are harvested (phv00222411.v6.p1)
HARVEST_QUANT - Amount of RNA harvested (phv00222424.v6.p1)
HIGH_THROUGHPUT_SEQUENCER - High throughput sequencer used (phv00222394.v6.p1)
HTSeq_version - HTSeq version used (phv00222439.v6.p1)
HumanGenomeAssembly - Human Genome assembly used (phv00222435.v6.p1)
IMAGE_DESCRIPTION - Image description (phv00222506.v6.p1)
IMAGE_DESCRIPTION - Image description (phv00222511.v6.p1)
IMAGE_FILENAME - Image filename. These files are all available publicly through the dbGaP FTP site: ftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000833. (phv00222507.v6.p1)
IMAGE_FILENAME - Image filename (phv00222512.v6.p1)
IMAGE_FILETYPE - File format (phv00222508.v6.p1)
IMAGE_FILETYPE - File format (phv00222513.v6.p1)
IMAGE_NOTES - Any additional remarks connected to the image (phv00222509.v6.p1)
IMAGE_NOTES - Any additional remarks connected to the image (phv00222514.v6.p1)
indexAdapter(first) - Number of first reads trimmed for the Index adapter (phv00222467.v6.p1)
indexAdapter(second) - Number of second reads trimmed for the Index adapter (phv00222468.v6.p1)
INPUT_AMOUNT - Input amount of RNA that goes in to library preparation (phv00222425.v6.p1)
IS_PAIRED? - Paired-end sequencing used? (phv00222396.v6.p1)
IS_polyA_SELECTED - Does the RNA go through poly(A) selection? (phv00222430.v6.p1)
IS_TUMOR - Tumor status (phv00222381.v6.p1)
LIBRARY_BY - Code for the person who prepared the library for sequencing (phv00222416.v6.p1)
LIBRARY_DATE - Library date (phv00222417.v6.p1)
LOADING_DYE - Loading dye (phv00222502.v6.p1)
MaxReadsPerGeneExonic - Maximum number of reads that are exonic per gene (phv00222491.v6.p1)
MaxReadsPerGeneIntronic - Maximum number of reads that are intronic per gene (phv00222497.v7.p1)
MULTI_FLOWCELLS? - Is the sample sequenced using multiple flowcells? (phv00222390.v6.p1)
MULTI_LANES? - Is the sample sequenced using multiple lanes? (phv00222389.v6.p1)
Multimapped - % Multimapped reads by STAR aligner (phv00222486.v6.p1)
nBelowPhredThreshold(first) - Number of first reads with Phred Score less than the threshold for at least one position (phv00222461.v6.p1)
nBelowPhredThreshold(second) - Number of second reads with Phred Score less than the threshold for at least one position (phv00222462.v6.p1)
nBothDiscarded - Number of read pairs discarded after trimming for being too short (< 20 nt) (phv00222458.v6.p1)
nBothTrimmed - Number of read pairs trimmed for contaminants (phv00222455.v6.p1)
NexteraXT_TransposaseRC(first) - Number of reads trimmed for 3' NexteraXT Transposase Reverse complement (phv00222479.v6.p1)
nFirstDiscarded - Number of first reads discarded after trimming for being too short (< 20 nt) (phv00222459.v6.p1)
nFirstTrimmed - Number of reads trimmed for contaminants (First reads) (phv00222456.v6.p1)
NGS_Protocol_FileName - Document that details the NGS processing pipeline applied to the SCAP-T samples (phv00222434.v6.p1)
NoExonicFeature - Number of reads that did not map to any exon as reported by HTSeq (phv00222492.v6.p1)
NoIntronicFeature - Number of reads that did not map to any intron as reported by HTSeq (phv00222498.v7.p1)
nSecondDiscarded - Number of second reads discarded after trimming for being too short (< 20 nt) (phv00222460.v6.p1)
nSecondTrimmed - Number of reads trimmed for contaminants (Second reads) (phv00222457.v6.p1)
nTotalReadPairs - Number of total reads from RNA-Sequencing (phv00222454.v6.p1)
nTSOFiltered(first) - Number of reads filtered for being the TSO primer concatemers (phv00222482.v6.p1)
NUM_PCR_CYCLES_cDNA - Number of PCR cycles used (phv00222428.v6.p1)
NUM_PCR_CYCLES_NEXTERA - Number of PCR cycles used (phv00222429.v6.p1)
NUMBER_aRNA_AMPLIFICATION_ROUNDS - Number of aRNA amplification rounds (phv00222427.v6.p1)
NumGenesExpressed - Number of genes with at least one exonic read (phv00222489.v6.p1)
NumGenesWithIntronicExpression - Number of genes with at least one intronic read (phv00222495.v7.p1)
OPERATOR - Code for the person who operated the sequencer (phv00222399.v6.p1)
PennSCAP-T_pipeline_version - Version of the Penn SCAP-T pipeline (phv00222437.v6.p1)
PROTOCOL_A_FILENAME - Protocol A Filename (If applicable) (phv00222406.v6.p1)
PROTOCOL_A_NAME - Protocol A Name (If applicable) (phv00222405.v6.p1)
PROTOCOL_B_FILENAME - Protocol B Filename (If applicable) (phv00222408.v6.p1)
PROTOCOL_B_NAME - Protocol B Name (If applicable) (phv00222407.v6.p1)
PROTOCOL_C_FILENAME - Protocol C Filename (If applicable) (phv00222410.v6.p1)
PROTOCOL_C_NAME - Protocol C Name (If applicable) (phv00222409.v6.p1)
PUTATIVE_CELL_TYPE - Specifies the cell class. For instance neuron, cardiomyocyte, brown adipose tissue, etc. (phv00222418.v6.p1)
READ_LENGTH - Read length (phv00222395.v6.p1)
ReadsCountedExonic - Number of reads counted by HTSeq as exonic (phv00222488.v6.p1)
ReadsCountedIntronic - Number of reads counted by HTSeq as intronic (phv00222494.v7.p1)
ReadsTooShort - % Reads too short and not mapped as reported by STAR aligner (phv00222487.v6.p1)
removed3N(first) - Number of first reads trimmed for Ns from 3' end (phv00222465.v6.p1)
removed3N(second) - Number of second reads trimmed for Ns from 3' end (phv00222466.v6.p1)
removed5N(first) - Number of first reads trimmed for Ns from 5' end (phv00222463.v6.p1)
removed5N(second) - Number of second reads trimmed for Ns from 5' end (phv00222464.v6.p1)
RIBOSOMAL_DEPLETION_KIT - Ribosomal depletion kit used (phv00222431.v6.p1)
RNASEQ_COMMENTS - Additional comments on the sequencing for the sample (phv00222400.v6.p1)
RNASEQ_GRP - ID that groups the samples that were sequenced on the same flowcell (phv00222391.v6.p1)
SAMPLE_HARVEST_BY - Code for the person who harvested the cells (phv00222412.v6.p1)
SAMPLE_HARVEST_DATE - Harvest date (phv00222413.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222433.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222379.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222500.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222510.v6.p1)
Samtools_version - Samtools version used (phv00222442.v6.p1)
SEQ_CENTER - Sequencing Center (phv00222392.v6.p1)
SEQUENCING_DATE - Sequencing date (phv00222398.v6.p1)
SEQUENCING_PLATFORM - Sequencing platform (phv00222393.v6.p1)
SLICE_ID - Identifier to indicate the samples collected from the same slice of the biopsy (phv00222383.v6.p1)
SOURCE_REGION - Region of cell from where the input comes from (phv00222422.v6.p1)
SOURCE_TYPE - Cell source (phv00222420.v6.p1)
SOURCE_UNIT - Unit of source from where the sample material comes from (phv00222421.v6.p1)
SpikeInDilution - SpikeIn Dilution (phv00251848.v5.p1)
SpikeInType - SpikeIn Type (if it is used) (phv00251847.v5.p1)
STAR_version - STAR version used (phv00222438.v6.p1)
SURGEON - Randomly picked code for the surgeon who did the biopsy (phv00222386.v6.p1)
SURGERY_YEAR - Year of surgery (phv00222387.v6.p1)
TREATMENT - Any special treatment that the cell went through - such as TIVA (phv00222423.v6.p1)
UniqMap - % Uniquely mapped reads by STAR aligner (phv00222485.v6.p1)
univAdapterRC(first) - Number of first reads trimmed for the reverse complement of the Universal adapter (phv00222469.v6.p1)
univAdapterRC(second) - Number of second reads trimmed for the reverse complement of the Universal adapter (phv00222470.v6.p1)