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Recent Replies
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C: Variant not annotated by ANNOVAR in the main transcript by
geocarvalho • 170
Item 10 from ANNOVAR FAQ talks about precedence and other possibilities: > (1) the use of di...
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C: Get species/genus names from NCBI nr protein accession IDs for phylogenetic tree by
GenoMax ♦ 94k
You could do something like following using [EntrezDirect:][1] $ esearch -db protein -query ...
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C: Software/Package to automatically annotate genes? Do any exist? by
rpolicastro ♦ 3.2k
I'm not sure if there are any databases beyond some curated ones that will have one word descript...
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C: Blast + Alignement Shell Script by
lieven.sterck ♦ 9.4k
Not saying that this BIRCH interface might not have its merits but most often if you want to writ...
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C: only one biological read present in fastq NCBI database for paired-end sequencin by
Matt • 10
Thank you very much for this answer, very clear very complete, i successfully used Cellranger wit...
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A: scRNA-seq, MONOCLE3, and trajectory reconstruction, and Moran I statistics by
volkanergin • 0
Thanks, I'll look through it.
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C: TCGABioLinks getManifest() function. How to alter saved file name? by
_r_am ♦ 32k
The code for `getManifest` is: getManifest <- function(query, save = FALSE) { man...
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A: Blast + Alignement Shell Script by
brian.fristensky • 130
Rather than writing a shell script, you might want to try out the extensive features in the [BIRC...
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C: Bulk RNAseq data for COVID-19 with patient metadata? by
GenoMax ♦ 94k
Take a look at this resource: https://outbreak.info/ In any case, patient metadata is unlikely t...
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A: only one biological read present in fastq NCBI database for paired-end sequencin by
Matt • 10
Thank you very much for this answer, very clear very complete, i successfully used Cellranger wit...
-
C: Getting alignments with lower scores on Biopython by
trinityduke100 • 10
Is there a way to find alignments of lower scores apart from the method I mentioned above which a...
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A: Adding gene names to fasta file by
Joe ♦ 18k
Here's a biopython solution: from Bio import SeqIO import sys with open(sys.arg...
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