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What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
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Recent Replies
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
melissa.joubert
• 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
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