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Recent Replies
Comment: NarrowPeak format -Peak field
by
ATpoint
72k
I do not follow, can you please add a chr-start-end example.
Comment: BioPython: convert fasta to fastq without quality score input file
by
capemaster
•
0
The command with `gawk` is:
awk 'BEGIN {RS = ">" ; FS = "\n"} NR > 1 {print $1"\n"$2"\n+\n"gensub(/./, "I", "g", $2)}'
Comment: The inchworm process failed. Trinity running error.
by
GenoMax
129k
So with 600M reads you will need a minimum of 600GB of RAM per trinity recommendations.
If you are not able to get more memory consider no…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
I don't understand what you're saying. Your allele is different from the ref allele so it needs the sample to support that? Why?
Give me t…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
mohsamir2016
▴
30
Sure, but n my case 1/1 the allel is different from the reference allele and it called it as T, for instance. So it needs reads in the samp…
Comment: The inchworm process failed. Trinity running error.
by
andres.firrincieli
3.3k
can you run the same command with just one sample with the flag `--verbose` so we can actually see the error?
Comment: ggsave() bug in ggplot2?
by
Medeea
•
0
Thank you very much for your suggestion, I have tried with units = "cm" and still it is not saved at desired dpi.
I also ran your example …
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
I've removed irrelevant tags from your post.
Answer: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
Ref alleles are from the reference genome. GATK doesn't need a read supporting the ref genome on a sample to know what the ref base is at a…
Comment: Single Cell Rna Seq Using BD Rhapsody
by
Ram
39k
What does this have to do with Rhapsody scRNA?
Also, why are you recommending DESeq2 for scRNA DE analysis?
Comment: The inchworm process failed. Trinity running error.
by
Marta
•
0
My bad, its 600 millions reads, 15-20 per sample. I meant that in this case, I run the code with all samples merged. However, using only on…
Comment: how to look for interactions between different chromosomes
by
Buffo
★
2.2k
I don't think it is possible. HiC resolution is limited even for intra-chromosome interactions, and most bioinformatic tools discard reads …
Comment: Single Cell Rna Seq Using BD Rhapsody
by
dsull
★
4.2k
I'm referring to non-multiplexed data where the only thing you need to deal with are the three 9-bp cell barcodes separated by linkers. I t…
Comment: What is NCBI Gene ID, where to find it and how to convert to entrez ID?
by
GenoMax
129k
@Pegasus you are not going to be able to get Entrez ID for the data you have (pretty sure this question is following up on https://www.bios…
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