Single Cell Analysis Program - Transcriptome (SCAP-T) (U. Penn)

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Other (128)

3polyA(first) - Number of first reads trimmed for polyA from 3' end (phv00222227.v6.p1)
3polyA(second) - Number of second reads trimmed for polyA from 3' end (phv00222228.v6.p1)
5polyT(first) - Number of first reads trimmed for polyT from 5' end (phv00222225.v6.p1)
5polyT(second) - Number of second reads trimmed for polyT from 5' end (phv00222226.v6.p1)
ADDITIONAL_SAMPLE_COMMENTS - Additional sample comments (phv00222182.v6.p1)
AmbiguousMappedExonic - Number of reads that mapped ambiguosly to exons of more than one gene and were not counted (phv00222243.v6.p1)
AmbiguousMappedIntronic - Number of reads that mapped ambiguosly to introns of more than one gene and were not counted (phv00222287.v7.p1)
ANALYTE_TYPE - Analyte type (phv00222130.v6.p1)
aRNAPrimer(first) - Number of first reads trimmed for the aRNA primer (phv00222221.v6.p1)
aRNAPrimer(second) - Number of second reads trimmed for the aRNA primer (phv00222222.v6.p1)
aRNAPrimerRC(first) - Number of first reads trimmed for the reverse complement of aRNA primer (phv00222223.v6.p1)
aRNAPrimerRC(second) - Number of second reads trimmed for the reverse complement of aRNA primer (phv00222224.v6.p1)
AvgInpReadLen - Average read length (phv00222233.v6.p1)
AvgReadPerGeneExonic - Average number of reads that are exonic per gene (phv00222240.v6.p1)
AvgReadPerGeneIntronic - Average number of reads that are intronic per gene (phv00222284.v7.p1)
AvgUniqMapLen - Average read length for uniquely mapped reads (phv00222234.v6.p1)
BARCODE - Unique sequence that is part of the Illumina barcode (phv00222176.v6.p1)
BIOPSY_COMMENTS - Any comments from the surgeon who carried out the biopsy (phv00222138.v6.p1)
BIOPSY_ID - Identifier to indicate the samples collected from the same biopsy (phv00222132.v6.p1)
BLAST_Bacteria - Number of BLAST matches to Bacteria (phv00222195.v6.p1)
BLAST_ERCC - Number of BLAST matches to ERCC (phv00222203.v6.p1)
BLAST_Fish - Number of BLAST matches to Fish (phv00222196.v6.p1)
BLAST_Fly - Number of BLAST matches to Fly (phv00222197.v6.p1)
BLAST_HitsNotCounted - Number of BLAST matches to any other species (phv00222202.v6.p1)
BLAST_HitsNotTarget_or_ERCC - Percentage hits that map neither to the Human genome nor to ERCC sequences (phv00222194.v6.p1)
BLAST_Human - Number of BLAST matches to Human (phv00222198.v6.p1)
BLAST_Mouse - Number of BLAST matches to Mouse (phv00222199.v6.p1)
BLAST_Rat - Number of BLAST matches to Rat (phv00222200.v6.p1)
BLAST_TotalHits - The number of reads out of 5000 randomly selected reads that map against the nt database using BLAST (phv00222193.v6.p1)
BLAST_version - Blast version used (phv00222190.v6.p1)
BLAST_Yeast - Number of BLAST matches to Yeast (phv00222201.v6.p1)
BODY_SITE - Body site where sample was collected (phv00222134.v6.p1)
C1_ADDITIONAL_REAGENTS_ADDED - Additional reagents added besides the standard (phv00222154.v6.p1)
C1_CHIP - C1 Chip information (phv00222153.v6.p1)
C1_EXP_ID - Unique ID to identify samples that were collected using the same C1 experiment (if applicable) (phv00222151.v6.p1)
C1_SAMPLE_LOAD - Fresh/Frozen nuclei loaded on the C1 chip (phv00222152.v6.p1)
cDNA_BY - Code for the person who prepared the cDNA (phv00222164.v6.p1)
cDNA_DATE - CDNA preparation date (phv00222165.v6.p1)
CDS_RC(first) - Number of reads trimmed for the CDS 3' Adapter Reverse complement (phv00222231.v6.p1)
CDS(first) - Number of reads trimmed for the CDS 3' Adapter (phv00222230.v6.p1)
CELL_SUBCLASS - Specifies the cell sub-class. For instance: pyramidal, 5-HT, interneuron (phv00222169.v6.p1)
DEMULTIPLEXER - Demultiplexer used (phv00222147.v6.p1)
FastQC_version - FastQC version used (phv00222191.v6.p1)
FMAID - Foundational Model of Anatomy ID for the body site where the biopsy is taken from (phv00222135.v6.p1)
GencodeVersion - Gencode version (phv00222186.v6.p1)
HARVEST_METHOD - Method by which cells are harvested (phv00222161.v6.p1)
HARVEST_QUANT - Amount of RNA harvested (phv00222174.v6.p1)
HIGH_THROUGHPUT_SEQUENCER - High throughput sequencer used (phv00222144.v6.p1)
HTSeq_version - HTSeq version used (phv00222189.v6.p1)
HumanGenomeAssembly - Human Genome assembly used (phv00222185.v6.p1)
IMAGE_DESCRIPTION - Image Description (phv00222245.v5.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. (phv00222246.v5.p1)
IMAGE_FILETYPE - File format (phv00222247.v5.p1)
IMAGE_NOTES - Any additional remarks connected to the image (phv00222248.v5.p1)
indexAdapter(first) - Number of first reads trimmed for the Index adapter (phv00222217.v6.p1)
indexAdapter(second) - Number of second reads trimmed for the Index adapter (phv00222218.v6.p1)
INPUT_AMOUNT - Input amount of RNA that goes in to library preparation (phv00222175.v6.p1)
IS_PAIRED? - Paired-end sequencing used? (phv00222146.v6.p1)
IS_polyA_SELECTED - Does the RNA go through poly(A) selection? (phv00222180.v6.p1)
IS_TUMOR - Tumor status (phv00222131.v6.p1)
LIBRARY_BY - Code for the person who prepared the library for sequencing (phv00222166.v6.p1)
LIBRARY_DATE - Library date (phv00222167.v6.p1)
MaxReadsPerGeneExonic - Maximum number of reads that are exonic per gene (phv00222241.v6.p1)
MaxReadsPerGeneIntronic - Maximum number of reads that are intronic per gene (phv00222285.v7.p1)
MULTI_FLOWCELLS? - Is the sample sequenced using multiple flowcells? (phv00222140.v6.p1)
MULTI_LANES? - Is the sample sequenced using multiple lanes? (phv00222139.v6.p1)
Multimapped - % Multimapped reads by STAR aligner (phv00222236.v6.p1)
nBelowPhredThreshold(first) - Number of first reads with Phred Score less than the threshold for at least one position (phv00222211.v6.p1)
nBelowPhredThreshold(second) - Number of second reads with Phred Score less than the threshold for at least one position (phv00222212.v6.p1)
nBothDiscarded - Number of read pairs discarded after trimming for being too short (< 20 nt) (phv00222208.v6.p1)
nBothTrimmed - Number of read pairs trimmed for contaminants (phv00222205.v6.p1)
NexteraXT_TransposaseRC(first) - Number of reads trimmed for 3' NexteraXT Transposase Reverse complement (phv00222229.v6.p1)
nFirstDiscarded - Number of first reads discarded after trimming for being too short (< 20 nt) (phv00222209.v6.p1)
nFirstTrimmed - Number of reads trimmed for contaminants (First reads) (phv00222206.v6.p1)
NGS_Protocol_FileName - Document that details the NGS processing pipeline applied to the SCAP-T samples (phv00222184.v6.p1)
NoExonicFeature - Number of reads that did not map to any exon as reported by HTSeq (phv00222242.v6.p1)
NoIntronicFeature - Number of reads that did not map to any intron as reported by HTSeq (phv00222286.v7.p1)
nSecondDiscarded - Number of second reads discarded after trimming for being too short (< 20 nt) (phv00222210.v6.p1)
nSecondTrimmed - Number of reads trimmed for contaminants (Second reads) (phv00222207.v6.p1)
nTotalReadPairs - Number of total reads from RNA-Sequencing (phv00222204.v6.p1)
nTSOFiltered(first) - Number of reads filtered for being the TSO primer concatemers (phv00222232.v6.p1)
NUM_PCR_CYCLES_cDNA - Number of PCR cycles used (phv00222178.v6.p1)
NUM_PCR_CYCLES_NEXTERA - Number of PCR cycles used (phv00222179.v6.p1)
NUMBER_aRNA_AMPLIFICATION_ROUNDS - Number of aRNA amplification rounds (phv00222177.v6.p1)
NumGenesExpressed - Number of genes with at least one exonic read (phv00222239.v6.p1)
NumGenesWithIntronicExpression - Number of genes with at least one intronic read (phv00222283.v7.p1)
OPERATOR - Code for the person who operated the sequencer (phv00222149.v6.p1)
PennSCAP-T_pipeline_version - Version of the Penn SCAP-T pipeline (phv00222187.v6.p1)
PROTOCOL_A_FILENAME - Protocol A Filename (If applicable) (phv00222156.v6.p1)
PROTOCOL_A_NAME - Protocol A Name (If applicable) (phv00222155.v6.p1)
PROTOCOL_B_FILENAME - Protocol B Filename (If applicable) (phv00222158.v6.p1)
PROTOCOL_B_NAME - Protocol B Name (If applicable) (phv00222157.v6.p1)
PROTOCOL_C_FILENAME - Protocol C Filename (If applicable) (phv00222160.v6.p1)
PROTOCOL_C_NAME - Protocol C Name (If applicable) (phv00222159.v6.p1)
PUTATIVE_CELL_TYPE - Specifies the cell class. For instance neuron, cardiomyocyte, brown adipose tissue, etc. (phv00222168.v6.p1)
READ_LENGTH - Read length (phv00222145.v6.p1)
ReadsCountedExonic - Number of reads counted by HTSeq as exonic (phv00222238.v6.p1)
ReadsCountedIntronic - Number of reads counted by HTSeq as intronic (phv00222282.v7.p1)
ReadsTooShort - % Reads too short and not mapped as reported by STAR aligner (phv00222237.v6.p1)
removed3N(first) - Number of first reads trimmed for Ns from 3' end (phv00222215.v6.p1)
removed3N(second) - Number of second reads trimmed for Ns from 3' end (phv00222216.v6.p1)
removed5N(first) - Number of first reads trimmed for Ns from 5' end (phv00222213.v6.p1)
removed5N(second) - Number of second reads trimmed for Ns from 5' end (phv00222214.v6.p1)
RIBOSOMAL_DEPLETION_KIT - Ribosomal depletion kit used (phv00222181.v6.p1)
RNASEQ_COMMENTS - Additional comments on the sequencing for the sample (phv00222150.v6.p1)
RNASEQ_GRP - ID that groups the samples that were sequenced on the same flowcell (phv00222141.v6.p1)
SAMPLE_HARVEST_BY - Code for the person who harvested the cells (phv00222162.v6.p1)
SAMPLE_HARVEST_DATE - Harvest date (phv00222163.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222183.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222129.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222244.v5.p1)
Samtools_version - Samtools version used (phv00222192.v6.p1)
SEQ_CENTER - Sequencing Center (phv00222142.v6.p1)
SEQUENCING_DATE - Sequencing date (phv00222148.v6.p1)
SEQUENCING_PLATFORM - Sequencing platform (phv00222143.v6.p1)
SLICE_ID - Identifier to indicate the samples collected from the same slice of the biopsy (phv00222133.v6.p1)
SOURCE_REGION - Region of cell from where the input comes from (phv00222172.v6.p1)
SOURCE_TYPE - Cell source (phv00222170.v6.p1)
SOURCE_UNIT - Unit of source from where the sample material comes from (phv00222171.v6.p1)
SpikeInDilution - SpikeIn Dilution (phv00252228.v5.p1)
SpikeInType - SpikeIn Type (if it is used) (phv00252227.v5.p1)
STAR_version - STAR version used (phv00222188.v6.p1)
SURGEON - Randomly picked code for the surgeon who did the biopsy (phv00222136.v6.p1)
SURGERY_YEAR - Year of surgery (phv00222137.v6.p1)
TREATMENT - Any special treatment that the cell went through - such as TIVA (phv00222173.v6.p1)
UniqMap - % Uniquely mapped reads by STAR aligner (phv00222235.v6.p1)
univAdapterRC(first) - Number of first reads trimmed for the reverse complement of the Universal adapter (phv00222219.v6.p1)
univAdapterRC(second) - Number of second reads trimmed for the reverse complement of the Universal adapter (phv00222220.v6.p1)