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|Interface||Command line interface|
|Restrictions to use||None|
|Output format||SAM, tab-delimited text|
|License||GNU General Public License version 2.0|
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- person_outline Felix Krueger
Publication for Bismark
B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation
[…] RRBS FASTQ files were quality trimmed using FastQC (v0.11.5) and mapped to the mouse genome (mm9) using Bismark (v0.16.3) using the following options: “--bam --chunkmbs 1024 –multicore 8”. Mapped BAM files were sorted with SAMtools (v0.1.19-96b5f2294a) and methylation calls were extracted using the “Rsa […]
Genome wide profiling of long non coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening
[…] nome bisulfite sequencing data sets derived from 39 dpa and 52 dpa fruit were retrieved from the SRA database (SRA046092). Raw sequence data were mapped to the tomato genome assembly build 2.50 using Bismark 0.16.3  with the Bowtie2 (version 2.2.8) alignment tool . The percent methylation of cytosines in a CpG, CHG or CHH context was calculated by the proportion of 100* (methylated reads)/ (me […]
Clinical Remission of Sight Threatening Non Infectious Uveitis Is Characterized by an Upregulation of Peripheral T Regulatory Cell Polarized Towards T bet and TIGIT
[…] te the molarity of the library before sequencing. 150-bp Paired-end sequencing was performed using the Miseq Illumina sequencer (Illumina, Inc.) to a total of 400,000 reads passing filter per sample. Bismark () was used to align bisulfite-treated reads to a human reference genome and calculate the cytosine methylation calls at the target sites. Biostatistical analysis generated beta (%) methylatio […]
Long ncRNA A ROD activates its target gene DKK1 at its release from chromatin
[…] sequencing in MCF-7 cells was done using the SureSelect Methyl-Seq Target Enrichment System from Agilent. Data analysis (including read mapping, deduplication and methylation calling) was done using Bismark. Data available under GEO (NCBI) accession number GSE69505. […]
Association and cis mQTL analysis of variants in CHRNA3 A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population
[…] as identified using the Illumina HiSeq X Ten platform with an average of about 700 million (±75 million) 150-bp paired-end reads per sample. Clean reads were mapped to the hg19 reference genome using Bismark. We first combined two strands of information of CpG sites and then excluded those CpGs with <5 reads or that overlapped with common variants in the Chinese Han genome (MAF > 0.05). The MAF of […]
Data quality of whole genome bisulfite sequencing on Illumina platforms
[…] nd of R1 to remove bases derived from the sequence tag introduced in the library preparation procedure. Alignment to the human reference assembly GRCh37 and methylation calling was performed with the Bismark software  and the pipeline tool ClusterFlow . For TSDM libraries the initial 6 base pairs of each reads were ignored in the methylation calling procedure, to avoid random priming biases. G […]
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If I really want to nitpick and find a negative point, I would say the parallelization is a bit of a hassle if you have limited resources, it's not as straightforward as setting the number of threads to use, you need some experimenting with parameters like --multicore and -p to find out how many actual cores (and RAM) are used for a typical run with your settings. Also, itás not the fastest tool in the world, for example BSMAP is said to be faster (especially in RRBS mode), but then again in side-by-side comparisons I always managed to map more reads with Bismark, and I think the speed is quite reasonable, I'm happy with it.
Overall Bismark is a wonderful tool, I can highly recommend it for any (RR)BS data analysis!