Yoshiaki Yasumizu

Hi, thank you for the exciting tool. We are trying to conduct CalcPairwiseDistances and in TRA, TRB, TRD, it worked, but in other genes an error occurred. Is there a...

Hi, thank you for developing a great tool! I have a reference panel made by using scanpy and harmonypy, and considering performing query mapping of seurat objects using symphony. Do...

cwl

6

cwlでつくる？ ymlでinput情報を揃える。 working dir等どうすればいい？ - https://github.com/Barski-lab/workflows/blob/master/tools/trimgalore.cwl - https://github.com/common-workflow-language/workflows/tree/master/tools - https://github.com/roryk/salmon-cwl /tools にまとめてtool.cwlはまとめる？ mouse, humanとPE,SE分ける。とりあえずIlluminaだけで。 wgetでreferenceとるのも。

fileが RAW_C_1_1.fastq.gz みたいな名前だったので experimental_matrix.csv の fastq(PREFIX) の欄に RAW_C_1 と書きました それで動かすと ``` + '[' false = true ']' + MAX_SPOT_ID= + echo experimental_matrix.csv experimental_matrix.csv + cat experimental_matrix.csv RAW_3H3,3H_3,PE,activated+ [[ -f tximport_R.R...

`fasterq-dump SRRID`だとNCBIから直接ダウンロードになって遅い。DDBJからapiを使って.sraを落としてfasterq-dumpで展開するように書き換える。

RSeQC

1

http://rseqc.sourceforge.net/ http://kazumaxneo.hatenablog.com/entry/2018/02/27/235531 multiqcでも表示できそう https://multiqc.info/docs/ Supported scripts: - bam_stat - gene_body_coverage - infer_experiment - inner_distance - junction_annotation - junction_saturation - read_distribution - read_duplication - read_gc

When parsing a virus-less file, an error occurs in pd.read_csv. https://github.com/yyoshiaki/VIRTUS/blob/master/tool/mk_summary_virus_count/mk_summary_virus_count.py

Hello, I would like to use alevin for quantification of 10x 5' PE. 10x 5' PE contains cDNA in read1 as well as read2. Could you tell me how to...

--gene_name ensembl or symbol

Consideration of ERV splicing events.

2

Hi, I would like to ask about the splicing events of ERV. mRNAs from ERV are sometimes spliced, but in the article, you executed telescope for the bam files generated...