3), REPdenovo (Chu et al. 2016), and ChIPtigs from ChIP-seq data (He et al. 2015). These methods rely on k-mers rather than alignments to build contigs, but in doing so less-frequent and rare k-mers may be lost in the final assembled contigs. While none of these methods offer...
The sequencing ready library was purified with SPRIselect, quality controlled for sized distribution and yield (LabChip GX Perkin Elmer), and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824). Finally, the sequencing was done using Illumina HiSeq...
https://doi.org/10.1016/j.celrep.2019.01.063 Cell Reports 26, no. 7 (February 2019): 1951-1964.e8. Scanpy - Python-based pipeline for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression and network simulation Paper Wolf, F. Alexander, Philipp ...
Cell Rep. 10, 2069–2082 (2015). Article CAS Google Scholar Williams, Z. et al. Discovery and characterization of piRNAs in the human fetal ovary. Cell Rep. 13, 854–863 (2015). Article CAS Google Scholar Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & ...
Sci Rep. 2015;5:12748. Article CAS PubMed PubMed Central Google Scholar Wiseman RW, Karl JA, Bimber BN, O’Leary CE, Lank SM, Tuscher JJ, Detmer AM, Bouffard P, Levenkova N, Turcotte CL, Szekeres E Jr, Wright C, Harkins T, O'Connor DH. Major histocompatibility complex genotyping...
{1..2}; do wget https://3d-seq-01.s3.us-west-2.amazonaws.com/fastq/gcsR-dddA-Para-dddI-delta-ung-0Ara-P3-rep${x}_${y}.fastq.gz ; done ; done $ cd ../ $ python3 AlignReads -n 8 fastq NCBI/Pseudomonas_aeruginosa_PAO1_GCF_000006765.1 tmf $ python3 Process3DSeq -n 3 ...
Cell Rep., 25 (2018), pp. 236-248.e6 View PDFView articleView in ScopusGoogle Scholar Law et al., 2014 C.W. Law, Y. Chen, W. Shi, G.K. Smyth voom: Precision weights unlock linear model analysis tools for RNA-seq read counts Genome Biol., 15 (2014), p. R29 View in Scopus...
Loudon, B. Berry, N. Richoz, J. Jones, X. Tan, et al. Resolving the immune landscape of human prostate at a single-cell level in health and cancer Cell Rep, 37 (2021), Article 110132, 10.1016/j.celrep.2021.110132 View PDFView articleView in ScopusGoogle Scholar [37] D. van Dijk,...
Sci Rep. 2016;6:25533. Article PubMed PubMed Central CAS Google Scholar Bansal V. A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments. BMC Bioinformatics. 2017;18:43. Article PubMed PubMed Central CAS Google Scholar Sayols S, Scherzinger D, ...
chromatin profiles for SKNMC cells25,28(Fig.1dand Extended Data Fig.2a–f). In contrast to the genomic background (Extended Data Fig.1m,n), DisP-seq peaks were most frequently found in weak enhancer regions, followed by active enhancer regions (Fig.1e). The median levels of DisP-seq ...