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Recent Replies
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
by
GenoMax
150k
Original question was about nanopore data. Are you referring to PacBio HiFi data?
Answer: DiffBind normalization error: invalid argument type (list) - cannot make it work
by
Rory Stark
★
2.1k
If your peaks are in `narrowPeak` format, it may help to set the `PeakCaller` to `"narrow"`.
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
by
vkaz
•
0
@Matt -- Hi, did you figure out about the cause of poly-A spike in your reads? I have similar problem in genomic HiFi reads.
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
•
0
Okay so I used the command which you mentioned earlier, since I only want the reads which have a G to T substitution, I parsed the output s…
Comment: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
by
Paulo
•
0
Hi Istvan!
This was exactly what I was looking for! Amazing how 11 years after, this post is still usefull and active :)
I have a que…
Comment: Larger genome size than expected-please help
by
GenoMax
150k
> The problem is that they all have many contigs (over 300)
That may indicate that these may not be "complete/reference" quality. How many…
Answer: Larger genome size than expected-please help
by
Istvan Albert
102k
Genome assembly is still a trial and error process, but getting 39 million genomes for a 34-million-long expectation is not too bad.
Oft…
Comment: Larger genome size than expected-please help
by
alexandrakortsi
•
0
Because it is a very common species and there are 15 available genomes around the size i mentioned. The problem is that they all have many …
Comment: Larger genome size than expected-please help
by
GenoMax
150k
> if these extra million bp are real (seems unlikely)
Why do you feel that way? Have you aligned your assembly to an available reference…
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
•
0
yes! I am running it now
but your second suggestion: samtools view in.bam "chrX:124068651-124068651" | cut -f1 will give me all the read…
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
•
0
jup you are right sorry the updated bed file looks like this:
chrX 124068649 124068651
I then grep "124068651" res.txt > res_fil…
Comment: Find the reads which correspond to DP of vcf
by
Pierre Lindenbaum
165k
please try my samtools command above (fixed a few minutes ago, missing -h)
Comment: Find the reads which correspond to DP of vcf
by
Pierre Lindenbaum
165k
>reg.bed looks this way: chrX 124068651 124068651
it cannot work anyway, you should get an error message:
[WARN][BedLineCodec]cannot use …
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
•
0
java -jar /mnt/beegfs/sbhattacharya/clone_tracing/bam_file/M1/jvarkit/dist/jvarkit.jar sam2tsv -R GCA_000001405.15_GRCh38_no_alt_analys…
Comment: Find the reads which correspond to DP of vcf
by
Pierre Lindenbaum
165k
> And there are such 18683080 entries. It is not possible to have so many entries because we have performed nest
I wrote this tool, how di…
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