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Recent Replies
Comment: grep sequence
by
lieven.sterck
11k
apologies for that, it was missing a trailing / , fixed it in the cmdline above
Comment: grep sequence
by
saadleeshehreen
▴
70
Thanks but an Error is given. How to solve it?
sed: -e expression #1, char 6: unterminated `s' command
Comment: grep sequence
by
lieven.sterck
11k
as an additional note I want to add that I provided a working solution here but that you could have found this yourself doing some searchin…
Answer: grep sequence
by
lieven.sterck
11k
cat <yourFile> | paste - - | grep -v 'shuffled' | sed 's/\t/\n/g' > new_file
cat your file, put header and sequence on one line (paste…
Answer: Combine full-length and 3` RNAseq, is it possible?
by
ATpoint
49k
Definitely use the same within the same project and make sure all batches you ever produce and plan to analyse together have replicates of …
Comment: Comparing two variant files
by
prasundutta87
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480
Check out the bcftools manual (https://samtools.github.io/bcftools/bcftools.html#isec) in order to see if you are running the command corre…
Answer: Combine full-length and 3` RNAseq, is it possible?
by
mohammadalkadi0
▴
30
In my humbel exprience, any difference in the protocols or computional method would result in bias in the count. I don't recommend it.
Comment: RSEM Calculate Expression Error
by
mohammadalkadi0
▴
30
Sorry for late reply. "Invalid number of arguments"implied that you added more than the 4 arguments. the first arg is upstream_read_files (…
Answer: Warning message: 'channel' automatically added to varMetadata in phenoData.
by
mohammadalkadi0
▴
30
What I understood is that 'channel' is a column that should be in varMetadata. I guess since it was added automatically, no need to worry!
Comment: Merge 2 GTF using agat avoiding overlapping
by
Juke34
★
5.7k
AGAT cannot help here, as explained in the other thread it removes identical transcripts only if all level3 features (exon, CDS, UTR, etc) …
Comment: GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
by
kanika.151
▴
110
Hello,
total coverage = Total reads in the region specified (for all the samples)
mean coverage = Average reads per base in the region sp…
Comment: GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
by
kanika.151
▴
110
Hello,
Did you sort the file according to your reference genome?
Method used to download the refseq file: [GATK RefSeq file download ins…
Comment: can not understand algorithms
by
colindaven
★
2.8k
This is one of the best set of materials (and course) that I've seen on this topic:
http://www.langmead-lab.org/teaching-materials/
Comment: mutation analysis, tcga
by
Rob
▴
40
Lol, Of course you did not get my question.
there is no specific column with name "Amino acid change".
So, I don't know what other column …
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