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Recent Replies
Comment: Which companies/institutions allow you to use their servers for bioinformatics a
by
Jean-Karim Heriche
25k
> RNAseq tools have been depreciated in Galaxy
Not sure what you're referring to but there are definitely RNA seq tools in Galaxy, at leas…
Comment: Error of SAM file
by
Pish
•
0
I am sorry that I did not answer you to the point.
For the second time, yes, I did nohup.
> nohup bwa mem -t 32 ./bwa_ref/4_marker_bwa.fa…
Comment: ClusterProfiler : What is GeneRatio and BgRatio?
by
yatzutzu
•
0
I am also struggling with the same problem (i.e. n and N are changing). Have you figured it out?
Answer: How to compare Sars-Cov-2 RefSeq to Influenza A RefSeq
by
patrickdm
▴
120
> I'm trying to learn bioinformatics. As an exercise..
Because you mentioned fasta and Biopython, I'd suggest to start by learning how to …
Comment: Error of SAM file
by
Pierre Lindenbaum
145k
did you use something like "nohup" to launch the job ?
Comment: How to compare Sars-Cov-2 RefSeq to Influenza A RefSeq
by
Asaf
8.7k
Once you have the sequences it's a bit like comparing Moby Dick with A Tale of Two Cities, there are different levels of comparisons and di…
Comment: Error of SAM file
by
Pish
•
0
This is a command that I used to align.
> bwa mem -t 32 ./bwa_ref/4_marker_bwa.fasta
> ./../../ill_other_betta/orn5_1_pairend_trimmed.fast…
Comment: Are the top 50 features in heat map for each phenotype in dataset generated by G
by
TM
▴
20
I got it, thank you so much for your explaination!!
Answer: Error of SAM file
by
ATpoint
61k
The SAM seems to include some of the bwa stderr logs (this stuff starting in square brackets) please show the exact command that was used f…
Answer: enrichr
by
Laura
▴
50
Use it through [gget enrichr][1] for super easy use!
[1]: https://github.com/pachterlab/gget
Comment: DESeq2 use of factors for colData
by
swbarnes2
12k
I believe it will try to make a linear correlation between the logs of the counts and your numerical colData. But it's hard to know withou…
Comment: Difference in total gene counts between samples
by
swbarnes2
12k
I think it's glaringly obvious that library size is driving your first PC. I would not be at all confident that the typical techniques wil…
Answer: Retrieving ensembl protein length with biomart
by
Laura
▴
50
*[gget][1] seq* will return the nucleotide (option "gene") or amino acid (option "transcript") sequence and sequence length for any Ensembl…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Pierre Lindenbaum
145k
`$1`: https://www.gnu.org/software/gawk/manual/gawk.html#Fields
`/^@/`: https://www.gnu.org/software/gawk/manual/gawk.html#Regexp-Usage
`…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
I0110
▴
120
What is the "$1 ~ /^@/'" part for? Thanks!
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