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Recent Replies
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
•
0
yes, this seems to be the problem. I will try realigning to a version of hg38 without alt contigs.
Comment: Removing batch effect in time-series data
by
Álvaro
•
0
I performed a clustered heatmap and PCA for all samples and the different timepoints did not group together. However, my doubts come from a…
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
•
0
Strange, I wonder why. Could it have anything to do with the "chr20_KI270871v1_alt"?
Comment: BCFtools not calling variant, despite adequate coverage
by
Pierre Lindenbaum
162k
your read is discarded because mapping quality=0
Answer: Removing batch effect in time-series data
by
rfran010
▴
960
Have you performed more formal analysis? PCA, clustering, correlation, etc...
If you have a time dependent batch effect, I would expect …
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
•
0
I uploaded the sam file here if you want to take a look:
https://github.com/samtools/bcftools/issues/2211
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
•
0
The reads are not duplicates. I think the color might be due to also matching the chr20 alt contig but I'm not sure.
An example line from …
Comment: How to download a file from zenodo link without leaving terminal?
by
SlowSD
•
0
Okay, are you aware of any file access setting in zenodo by changing which this can work out?
Comment: BCFtools not calling variant, despite adequate coverage
by
mpiersonsmela
•
0
The output is:
chr20 63439704 G 23 ,,,,,aa,.A.A,,a,a.aA.aA FFFFFFFFkFFFFFFFFFFFFFF
Comment: How to download a file from zenodo link without leaving terminal?
by
Pierre Lindenbaum
162k
https://zenodo.org/records/11791175
> The record is publicly accessible, but files are restricted to users with access.
so, no.
Comment: Problem in input data loading in Structure
by
Mensur Dlakic
★
27k
Error messages are usually meant to be taken literally. It says that your first line has two fewer columns than the rest of your file. It p…
Comment: How to download a file from zenodo link without leaving terminal?
by
SlowSD
•
0
Still, a 6kb html file gets downloaded in the name of SRR396636.sra_1.fastq
Comment: How to download a file from zenodo link without leaving terminal?
by
Medhat
9.7k
Could you try `wget -L -O SRR396636.sra_1.fastq "https://zenodo.org/record/11791175/files/SRR396636.sra_1.fastq"`
Comment: NCBI vs Ensembl - Ortholog genes Information
by
José
▴
10
Very enlightening. Thank you so much for your detailed exaplanation.
Comment: bedtools coverage gives error received illegal bin number, but that number isn't
by
Rashedul Islam
▴
470
> sed 's/[^[:print:]\t]//g' infile >outfile
Worked for me
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