broadinstitute/Drop-seq

Issues

• SplitBamByCell doesn't validate outputs early enough

  #226 opened 4 years ago
  0

• Drop-seq Tools Application on Dataset with Non-dropseq Barcode Design

  #224 opened 4 years ago
  4

• Is that possible to skip the SamtoFastq and map with bam file directly

  #222 opened 4 years ago
  8

• Cell Barcode and UMI on both read 1 and read2

  #221 opened 4 years ago
  4

• DigitalExpression: save temporary files for further counting

  #220 opened 4 years ago
  2

• CreateIntervalsFiles - STAR needs more RAM

  #218 opened 4 years ago
  1

• polyAtrimming NullPointerException

  #217 opened 4 years ago
  4

• DigitalExpression very low read counts

  #216 opened 4 years ago
  0

• selection of base range parameter in drop-seq pipeline

  #215 opened 4 years ago
  2

• MergeBamAlignment -- Do not use this function to merge dictionaries with different sequences in them

  #212 opened 4 years ago
  4

• Knee-finding method used in Cell paper

  #211 opened 4 years ago
  1

• CD24A Expression Missing

  #208 opened 4 years ago
  14

• DetectBeadSubstitutionErrors does not preserve bowtie2 BAM tag values

  #207 opened 4 years ago
  4

• ConvertToRefFlat error due to 'Missing gene_name' of the gtf file

  #206 opened 4 years ago
  8

• Truncated File Error During Drop-seq_alignment.sh

  #193 opened 5 years ago
  2

• The output of DigitalExpress is an empty matrix.

  #190 opened 4 years ago
  12

• DigitalExpression Exception in thread "main" htsjdk.samtools.util.RuntimeIOException

  #187 opened 4 years ago
  5

• DigitalExpression command problem

  #185 opened 4 years ago
  3

• Mixed-species data filtering

  #181 opened 5 years ago
  4

• DigitalExpression empty output

  #180 opened 5 years ago
  2

• information regarding Barcode collapse

  #178 opened 4 years ago
  1

• DigitalExpression seems to be missing my GENE_NAME_TAG

  #174 opened 5 years ago
  2

• ReduceGTF Fails for RefSeq GTF

  #169 opened 5 years ago
  4

• DigitalExpression: java.lang.OutOfMemoryError: GC overhead limit exceeded Dumping heap to java_

  #167 opened 5 years ago
  4

• NullPointerException when running TagReadWithGeneFunction, Drop-seq protocol

  #166 opened 5 years ago
  9

• Error: DigitalExpression

  #164 opened 5 years ago
  2

• Quantification of splicing isoforms with DGE

  #163 opened 5 years ago
  4

• extract reads specific to a barcode

  #162 opened 5 years ago
  3

• TagReadWithGeneFunction with Chromosome disagreement

  #161 opened 5 years ago
  1

• TagReadWithGeneFunction v2.3.0, java.lang.NullPointerException

  #160 opened 5 years ago
  2

• output barcode collapse information

  #159 opened 5 years ago
  4

• BamTagHistogram gives same results for setting filter_pcr_duplicates either true or false

  #157 opened 5 years ago
  6

• Use of barcode whitelist to determine accuracy and correction of barcodes.

  #149 opened 5 years ago
  2

• TagBamWithReadSequenceExtended Error:reads not properly paired

  #148 opened 5 years ago
  3

• BamTagHistogram reports more barcodes than expected

  #142 opened 5 years ago
  6

• Retrieve Alignment stats (*Log.final.out)

  #138 opened 5 years ago
  2

• PolyATrimmer option USE_NEW_TRIMMER causes NullPointerException

  #137 opened 5 years ago
  4

• Results not Matching

  #136 opened 5 years ago
  4

• How exactly are UMIs used to dedupulicate?

  #135 opened 5 years ago
  1

• TagBamWithReadSequenceExtended:Base [10] was requested, but the read isn't long enough [CCCCAAATT]

  #134 opened 6 years ago
  9

• How to draw Fig 3A in your 2015 Cell paper?

  #124 opened 6 years ago
  6

• Check files before running

  #123 opened 6 years ago
  2

• How are `NUM_GENIC_READS`, `NUM_TRANSCRIPTS`, and `NUM_GENES` defined in DigitalExpression?

  #122 opened 6 years ago
  6

• Issue with TagBamWithReadSequenceExtended, NativeLibraryLoader, unable to load file

  #120 opened 6 years ago
  6

• TagBamWithReadSequenceExtended | Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/dropseqrna/cmdline/DropSeqMain : Unsupported major.minor version 52.0

  #116 opened 6 years ago
  7

• NUM_CORE_BARCODES influences the output of DigitalExpression

  #104 opened 5 years ago
  3

• TagBamWithReadSequenceExtended - add option to store barcode read phred scores for all bases (not just summary)

  #102 opened 6 years ago
  1

• Output file of BamTagHistogram

  #95 opened 6 years ago
  2

• NullPointerException in DetectBeadSubstitutionErrors

  #90 opened 6 years ago
  3

• How should the gtf file for `TagReadWithGeneFunction` be structured?

  #78 opened 6 years ago
  3