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Recent Replies
Answer: DNA to peptide translation and adding to csv file
by
Pierre Lindenbaum
138k
$ echo -e "2840,GTGGCCCGGGAGGCC\n291,GCATGTCCGTAGGTTCGT\n147,GCATGTCCG" | awk -F, 'function translate(S) {L=length(S);P="";for(i=1;i+2…
Comment: orient flipped reads - adapter ligation
by
PhilippFW
•
0
BBduk failed for an unknown reason, but I managed to select the correct reads using "je demultiplex" and used reformat.sh to reverse comple…
Answer: DNA to peptide translation and adding to csv file
by
Mensur Dlakic
★
13k
There are several assignment errors above that I won't discuss in detail - you should be able to figure it out from the corrected code belo…
Comment: PGS Catalog file does not have rsID
by
Sam
★
3.8k
The actual implementation of chr-id so far is rather iffy, in that if I remember correctly, the extraction and exclusion doesn't work as ex…
Comment: Awk merge txt with database based on match
by
Pierre Lindenbaum
138k
use `join` https://linux.die.net/man/1/join
Comment: PGS Catalog file does not have rsID
by
Jenish
▴
20
Thanks. Should there be any difference in how this would work vs when using SNP ids? The c:l to snp id mapping should be 1 to 1 right?
Answer: Per base sequence Quality in Fast QC report
by
Papyrus
★
1.4k
Congratulations, your data seem to be of very good quality. It is normal for quality to drop towards the 3' end of the reads due to various…
Comment: Unable to overcome troubles in whole exome analysis
by
vinayjrao
▴
200
Pierre, there was also a comment here that suggested me to grep `A01223:29:HY2N7DMXX:2:2306:22562:23375` from my fastq file, and when I tri…
Comment: BCFtools view -R function
by
julia.zollner
▴
10
Ok, thank you very much Ram. Really appreciate your help. I will try and find someon locally. Thank you, Julia
Comment: Phylogenetic Tree from Massive Multifasta Alignment?
by
Mensur Dlakic
★
13k
Just curious: any reason you have and use two accounts?
Answer: Phylogenetic Tree from Massive Multifasta Alignment?
by
Mensur Dlakic
★
13k
Unless you are starting a new classification (new tree of life?) or building some sort of public database, 30K sequences is completely unne…
Comment: For what command-line programs or workflows, do you need a graphical user interf
by
Carambakaracho
★
2.7k
At least I know quite some biologists that can do outstanding data interpretation as soon as the data is in Excel, but they don't know how …
Comment: grep command for fasta header
by
cpad0112
17k
Try
$ seqkit -w 0 grep -f header.txt -irp "(.*)|chr" test.fa
Comment: GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip)
by
842978151
•
0
Hi kevin！For getting reliable expression matrices, I wanna know how to process the two non-normalized data from GEO database(GSE98278 & GSE…
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