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Comment: A question about the raw RNA-seq processing workflow
by
Dr William Klubinski
▴
90
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity
by
Ben_Ensembl
★
2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post:
https://www.ensembl.inf…
Comment: conda: command not found: gatk.
by
bestone
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10
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
Comment: conda: command not found: gatk.
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Pierre Lindenbaum
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> how about all your previous questions ? take a time to validate the good answers
Comment: conda: command not found: gatk.
by
bestone
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10
I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install t…
Comment: conda: command not found: gatk.
by
Pierre Lindenbaum
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how about all your previous questions ? take a time to validate the good answers (green mark on the left).
https://www.biostars.org/p/9565…
Answer: No @hd header returned in sam file when running bwa mem
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the HD header is not generated by bwa, but you can add it using awk:
bwa (...) | awk '(NR==1) {printf("@HD\tVN:1.6\tSO:unknown\n");}{…
Comment: Ensembl vep singularity
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Kiran
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Hi I also pulled SIF image from docker,, Now how do i execute the VEP from singularity ?
Answer: No @hd header returned in sam file when running bwa mem
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GokalpC
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Your sam file is not coordinate sorted or converted to a bam. @HD tags come after a secondary tool such as samtools view or sort.
ANGSD…
Comment: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★
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It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome
by
Andy
•
0
Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
Answer: Mapping a predicted sequence to a genome
by
Mensur Dlakic
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If we are talking about organisms without introns, it is very simple. A tool to use is `tblastn` which can be accessed from the [**main BLA…
Comment: How to get information about promoter from bulk-RNAseq?
by
rfran010
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I'll just add what I did with my own dataset of ribo depleted RNA-seq:
I took predicted enhancer-promoter interaction datasets from UCSC a…
Answer: How to get information about promoter from bulk-RNAseq?
by
rfran010
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170
What type of RNA-seq data do you have?
With polyA, I think it will be hard to incorporate enhancer info without additional datasets.
…
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