DigitalExpression very low read counts
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Hi all,
I am trying to run DigitalExpression step but the counts in the matrix are very low.. All the steps have been following the Drop-seq cookbook. Have anyone experienced such low counts ?? Is this due to the quality of the sample or pipeline ??
Any input is greatly appreciated!
DGE command
resources/Drop-seq_tools-2.3.0/DigitalExpression
I=11_TagRead/SRR11862676_star_gene_exon_tagged.bam
O=12_DGE/SRR11862676_out_gene_exon_tagged.dge.txt.gz SUMMARY=12_DGE/SRR11862676_out_gene_exon_tagged.dge.summary.txt
NUM_CORE_BARCODES=100
summary txt output
htsjdk.samtools.metrics.StringHeader # DigitalExpression SUMMARY=12_DGE/SRR11862676_out_gene_exon_tagged.dge.summary.txt OUTPUT=12_DGE/SRR11862676_out_gene_ex$## htsjdk.samtools.metrics.StringHeader # Started on: Thu Oct 29 10:56:01 EDT 2020 ## METRICS CLASS org.broadinstitute.dropseqrna.barnyard.DigitalExpression$DESummary CELL_BARCODE NUM_GENIC_READS NUM_TRANSCRIPTS NUM_GENES AGTATGAATAGG 19 6 3
CGCAAATGAAGA 22 6 2
CGTTTCCTTACT 20 5 2
TTATATACTTTT 12 5 2
TAGTCTATAGGT 16 5 3
TAACCGGTGACA 11 5 3
GGTAGGTTTCTA 34 5 3
CCCGGTCTCAAA 12 5 2
CCCATGGTGACG 30 5 2
GCGCCTGACCTT 20 5 2
CAATTGAGAAAG 23 5 1
ATTGAGCACGCT 23 5 3
TAGAAGGTAAGC 14 4 2
AGCCCGAAAACG 12 4 2
CGCAAACTCTAA 12 4 4
AGTCGCTTTCAC 30 4 2
GGTGGTGTTAAC 11 4 2
ATCACTTTATCA 14 4 2