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Hi,
I tried running Cell Ranger 6 (latest version) on the simulated reads, but within two minutes before the alignment even began the following error message returned (the same run using Cell Ranger …
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@fnothaft has concerns (upon which he will elaborate) regarding the testing process.
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- [x] discuss shortly the pipeline and its configuration with MS
- [x] check fastp documentation bc paired end (PE) needs additional sequence_r parameter here https://github.com/epigen/atacseq_…
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Dear Dengfeng,
I am using purge_dups on a diploid canu assembly (haplotypes not collapsed during assembly because of high heterozygosity). I have run step 1-3 of the pipeline (I don't have an alter…
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Hi all,
I am using align_trim.py script to remove primers from the alignment. In me case, we have performed SARS2 amplification with v3 primer set, and then sequenced with illumina (Miseq).
I …
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Hi!
I am using this snp from illumina exm1615904... whe I use plink it only uses the name of the SNP to get the geenotype (eg, as in this case normal would be CC vs GC or GG).
When usign BEDmatri…
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Hello!
I would like to know if there are any estimations on how long it takes to end a RegScaf job.
Our job has been running for a week now with these parameters.
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thread, 96
short_seme_pe…
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Hi,
I have a question regarding using parental HiFi instead of Illumina data for a trio-phased assembly (all experiments done with recent versions of hifiasm and yak).
When doing this, we observed f…
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Dear Community,
I've been attempting to run Trinity unsuccessfully. My first attempt involved using the reads in *fq.gz format, however the file decompression using own Trinity scripts did not wor…
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Hi,
thanks for putting together a great resource for novices to genomics data analysis!
I would suggest changing the wording in the subsection "Align reads to reference genome". Currently it rea…