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>python encode_task_reproducibility.py \
> liver1_peaks.narrowPeak.gz,liver2_peaks.narrowPeak.gz \
> --peak-type narrowPeak \
> --prefix liver_rep \
> --chrsz genome_nomt.size --out-dir ./
ENCODE…
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Dear Professor,
I am currently planning to analyze transcriptome data from The Cancer Genome Atlas (TCGA) project using this R package for my analysis. Given the various data transformation options…
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Hi,
ltr_finder, ltrharvest and LTR_retriever are quite slow in centier pipeline (expecially when the genome size is large), would please modify the code to accept existing scn file or LTR_retrieve…
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the taxonomic analysis in #35 and the protein comparisons in #40 as well as the sample summaries in #42 can all be usefully done immediately after the gather and genome information is calculated.
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Hi!
I am running PASA with a 5 Gb genome size (alignment assembly step). I cannot make it working with pblat or GMAP for some reasons (could it be the big genome size?) but it seems that minimap2 can…
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Hi Tobias,
Thank you for creating the ITAG4.1 GO annotation for tomato! This is a valuable resource for the plant research community.
I am currently using your annotation to perform GO enric…
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Hi,
When I did run my analysis with 4C-ker and tryed to upload my data to the UCSC genome browser the genome browser claimed that my bed file end position to some chromosomes were bigger than the en…
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https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline/blob/70025d47d2aea47043effa63f4f5d619004c9c7c/tasks/Qc.wdl#L319
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hi,
I don't know how to modify the conf.yml.
the error
`------ Reading the VP info file: ./example/VPinfo.txt
------ Demultiplexing Fastq files based on VPinfo file
>>> Reading Fastq: A…
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Dear Shaked,
I got the following error while trying to run TRAPeS on my data.
2020-05-29 22:22:53.066237 Working on: PB_629_L001-hisat2-sorted
/usr/local/analysis/trapes/20191013-20ea562/bin/trape…