-
Jumping (>>1Kb inserts) reads are required to use AllPaths-LG. I'd look at the many other excellent assemblers without that requirement (though jumping reads are very useful for all assemblers) -
Hello,
<REF>/<DATA>/frag_reads_orig.fastb
<REF>/<DATA>/frag_reads_orig.qualb
<REF>/<DATA>/frag_reads_orig.pairs
<REF>/<DATA>/jump_reads_orig.fastb
<REF>/<DATA>/jump_reads_orig.qualb
<REF>/<DATA>/jump_reads_orig.pairs
These files are needed by the /arch/AllPathsLG/bin/PrepareAllPathsInputs.pl script used by allpaths. How do I make them? I only have short reads, no jump sequences.Leave a comment:
-
I would second the posting of your question to the user forum.
Use a computer that has access to the filesystem where your run is (could be the same host or another one). Run your pipeline again with the same arguments and add DRY_RUN=True to see what else needs doing.
Ignore any errors about the current module not being finished (which is true).
You can also cause it to output an HTML page with the pipeline as you've configured it with the parameter VIEW_PIPELINE_AND_QUIT=True.
Assuming you're not using the optional long jumps or long reads then you have about 14 modules to go.
Good luck!Leave a comment:
-
This a great question for the Allpaths-LG user forum: https://groups.google.com/a/broadins...ths-user-forumLeave a comment:
-
AllPaths workflow question
Hi all. I'm assembling a eukaryotic genome with AllPaths. It's been moving along nicely for nearly three weeks and I'm hoping that the end is near. However, I can't find information on the processes that still need to be accomplished. As of this morning, the package started with RemoveHighCNAligns. Does anyone know of a list of the processes involved in AllPaths so I can get an idea of where I am in the entire assembly process?
Thanks.
David
-
At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...09-26-2023, 06:26 AM -
Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...09-07-2023, 11:15 PM -
Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.
Whole Transcriptome RNA-seq
Whole transcriptome sequencing...08-31-2023, 11:07 AM
Leave a comment: