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We have a fly genome assembled from PacBio that we treated with Tigmint and want to scaffold with ARKS and LINKS using 10X data.
I have run the commands presented in "infos_for_message_to_arks_and_…
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Hello
I run the supernova using
```
supernova run --id=Yuc27M --fastqs=analyzing_fastq --maxreads=1080624478 --localcores=64
```
got the phased fasta file output using following command:
```…
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Hey @gavinha
Sorry I'm not super familiar with snakemake. The input of BAM files don't appear to be loading correctly. The bam file name doesn't appear in the samtools command in the bxtools call.…
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Lauren wrote earlier:
>> As a side note we do have a Makefile (Examples/arcs-make) which runs the whole ARCS pipeline, >> taking the reads and the draft assembly as input. Even if you don't want to u…
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Hi,
Thanks in advance for any help. I'm running arks `1.0.2`, but my question is in reference to documentation on generating the interleaved input using `longranger`. I tried running `longranger` (…
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I'm trying to process the 10X 1.3 Million Brain Cells from E18 Mice dataset using Alevin with compiled salmon version 0.12.0 using the gencode.vM19.pc_transcripts.fa.gz as reference (https://support.1…
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I am trying to use the `STRetch_wgs_bam_pipeline.groovy` pipeline with a previously generated BAM against GRCh38, targeting a specific set of STRs I have identified in a BED file. After taking an hour…
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I got the following error when running athena-meta v1.1:
```
2018-11-01 22:02:32 - ========== Exception ==========
2018-11-01 22:02:32 - Traceback (most recent call last):
2018-11-01 22:02:32 -…
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I'm running Arcs with Tigmint. It runs about 16 hours and crashes. I'm using Samtools-1.9. Longranger was used to create the interleaved barcoded file from a Chromium run. Taro.contigs.fa is assembled…
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I working on a plant genome (~220 Mb)
My starting point is an phased assembly from Pacbio reads with Falcon and Falcon Unzip (774 contigs)
Important : I have renamed the contigs names by simple nu…