Jorge Zamora

how many reads were polyG trimmed?

1

Hello OpenGene team, is there a way to know from the fastp logs how many reads were polyG trimmed? Many thanks! Jorge

Hey OpenGene team, I am using fastp to trim polyG in NextSeq reads. That is the only filtering I am interested at this point. I am wondering if with these...

annotate translocations with svtyper

2

Hello, I was wondering wether it is possible to annotate translocations with svtyper. In the header of the svtyper vcf output I see these types of SVs ##ALT= ##ALT= ##ALT=...

Hello Matthew, I see in the join demo that you pass a range object to SparkContext.parallelize https://github.com/jleetutorial/python-spark-streaming/blob/master/3_advanced/1_Stream-Stream%20Join%20Demo.ipynb In the Spark documentation it says that SparkContext.parallelize takes an iterable or a...

inconsistent quality strings in error free sam file

1

Hello Yunfei, This is probably an ART question rather than varsim but I have noticed that if you generate an error free sam by passing --art_options="--errfree" to varsim the generated...

reduce the number of simulated clipped reads

4

Hello, I was wondering if there is a way to control how many clipped reads are simulated via Varsim (or Art). Many thanks Jorge

Allow users to prescriptively modulate the interaction rates for specific coordinate pairs.

4

Hello sim3C developers, This is not an issue. I would to know if sim3C can take pairs of genomic coordinates for which quimeric reads are also simulated. Many thanks Jorge

tool used for annotations

1

Hi, Did you use any particular tool to annotate the images. I would like to use the same one. Thanks so much Jorge