ZHIDIHUAYUAN

snaptools align-paired-end error

1

Hi, when I ran the following command: /amber/users/myzhou/anaconda3/envs/ATAC/bin/snaptools align-paired-end \ --input-reference=hap1.fa \ --input-fastq1=sample1_all_L001_R1_001.dex.fastq.gz \ --input-fastq2=sample1_all_L001_R3_001.dex.fastq.gz \ --output-bam=sample1_hap1.bam \ --aligner=bwa \ --path-to-aligner=/anaconda3/envs/ATAC/bin \ --read-fastq-command=zcat \ --min-cov=0 \ --num-threads=40 \ --if-sort=True \...

Bug: the wrong peak called by macs2

2

Hi: I used the MACS2 to deal with the ATAC-seq. The command was `macs2 callpeak -t /Sh4-1.chr_filt_dedup_sortbyname_fixed_tn5.bedpe -f BEDPE -n Sh4-1 -g hs --outdir ./ -B --keep-dup all --call-summits` The...

Hi, I am new to dropest pipeline. When I try to correct UMI, I got the following: Does this mean that I don’t need to do UMI correcting?

allele mode with SNP information of a region in chr6

6

Hi, I am intersected in a region in chr6 and I only have the SNP information in this region. Can I used the allele-specific mode to study the differences of...

Hi, I have bam files aligned with STAR 2- PASS using the GENCODE fasta file and GENCODE annotation file. Then I want to assemble transcripts using the Refseq annotiation because...