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Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
Kevin Blighe
86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF
by
alejandrogzi
▴
30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF
by
alejandrogzi
▴
30
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other
by
alejandrogzi
▴
30
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
Answer: How Do I Convert From Bed Format To Gff Format?
by
alejandrogzi
▴
30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue
by
Solal
•
0
Writing a solution for anyone interested.
The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Qboy
•
0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴
50
Thanks.
I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
avelarbio46
▴
30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
> so I don't think the genome size is available.
Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output
by
睿紘
•
0
For additional information,
"Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴
50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴
50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929.
I just rem…
Comment: Understanding mother and father alleles in VCF file
by
c.
•
0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
Correct. Data that went into the assembly.
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