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Recent Replies
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴
100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file.
for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput
by
Ying
•
0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM
by
Mensur Dlakic
★
19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file?
by
kalavattam
▴
70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
jared.andrews07
★
13k
@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
pifferdavide
▴
100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column.
However, with anoth…
Answer: Get nucleotide sequence of assembled RNA transcripts
by
tomas4482
▴
140
1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing.
2. subset to interested region -> extract chi…
Answer: Error in downloading scRNA data from ENA with wget
by
GenoMax
117k
Probably nothing wrong. Looks like a configuration restriction on your local cluster. Your job gets submitted to a worker node. Job is then…
Comment: converting a DocumentTermMatrix to factor
by
cpad0112
20k
This post does not fit the theme of this forum.
Answer: Quick way to get a field such as QNAME from the last read in a bam file?
by
Pierre Lindenbaum
146k
get the last chromosome of the bam using `samtools idxstat in.bam` and then use the index:
`samtools view in.bam <NAME_OF_LAST_CHROM>| t…
Answer: Fast way to sort bam file by queryname similar to picard SortSam SORT_ORDER=quer
by
Pierre Lindenbaum
146k
I don't think there a software doing this "fast".
You could fork samtools and change the function that compare the name of the reads here:…
Comment: Error in making DESeq2 object
by
Tusharika
•
0
I tried the following code:
> type(database)
Output:
> "character"
What to do?
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