Moderator: JC
JC ♦ 8.0k
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Computational Biologist
Posts by JC
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2
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85
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... if the file is decompressed: `grep -A4 HISEQ:151:HHKH7BCXX:2:1203:18952:80029 file.fastq`
if the file is compressed: `zgrep -A4 HISEQ:151:HHKH7BCXX:2:1203:18952:80029 file.fastq.gz`
`man grep` can explain to you how to use it
...
written 1 day ago by
JC ♦ 8.0k
1
vote
3
answers
156
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3
answers
... A few weeks ago I have a similar case, so I reported to the NCBI staff who responded:
> This location became unsustainable long time ago and is not maintained. New data were not added for years.
> You need to use SRA Toolkit for downloading SRA data. Please refer to the Download guide: https: ...
written 11 days ago by
JC ♦ 8.0k
0
votes
0
answers
114
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0
answers
... You can have multiple cases, but mainly in individual calls you are also considering "personal" variants (only present in one individual), if you want something more complete, you can take a look into the Population calls in GATK https://software.broadinstitute.org/gatk/documentation/article.php?id= ...
written 25 days ago by
JC ♦ 8.0k
1
vote
1
answer
85
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1
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... Blasting that with megablast don't have any significant hit, using blastn it gives the [short hits][1] that you described, so I guess is just contamination.
[1]: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=H4P95KKS014 ...
written 25 days ago by
JC ♦ 8.0k
2
votes
1
answer
85
views
1
answers
... [Blasting][1] your sequence to NT, the best hit is a 16S from uncultured archaea (Score=641, Query cov=80%, E=6e-180, %identity=95.31%)
[1]: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=H4N85R03014 ...
written 25 days ago by
JC ♦ 8.0k
1
vote
1
answer
187
views
1
answers
Answer:
A: How to reshape a fasta file?
... `perl -pe 's/\n// unless (/>/)' < FASTA > LINEARFASTA` ...
written 28 days ago by
JC ♦ 8.0k
1
vote
1
answer
128
views
1
answers
... Strictly talking you are "adjusting" your inputs to have a better selection, that is not representing what is happening in your samples. Could be better to explore is some samples are too different or if some proteins as almost-zero values to remove them and reduce variability between samples. ...
written 28 days ago by
JC ♦ 8.0k
1
vote
3
answers
132
views
3
answers
Answer:
A: Numeric genotype to letters
... $ perl -lae 'for ($i=5;$i<=$#F;$i++) { $F[$i]=$F[3]x2 if ($F[$i]==0); $F[$i]=$F[3].$F[4] if ($F[$i]==1); $F[$i]=$F[4]x2 if ($F[$i]==2); $F[$i]=~ s/,.+//; } print join "\t", @F' < in
#CHROM START ID Ref Alt 108 139 159 265 350
5 5571 snp_5_55 ...
written 4 weeks ago by
JC ♦ 8.0k
2
votes
1
answer
107
views
1
answers
... Perl:
`perl -pe 's/\[db_xref=Ensembl.+?\]//g' < input > output` ...
written 5 weeks ago by
JC ♦ 8.0k
1
vote
1
answer
254
views
1
answers
... At some point, it could be cheaper just to sequence again the samples (if available) ...
written 5 weeks ago by
JC ♦ 8.0k
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