Moderator: JC

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JC8.0k
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Computational Biologist

Posts by JC

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Answer: A: know the grep command for fastq file
... 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 JC8.0k
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Answer: A: i can't find the SRR sample on NCBI FTP, such as SRR018260
... 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 JC8.0k
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Comment: C: Why do I have more than 5000 variants when I used a 5K snp array?
... 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 JC8.0k
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Comment: C: Suspicious feature from 16S rRNA gene analysis using archaeal primers
... 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 JC8.0k
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Answer: A: Suspicious feature from 16S rRNA gene analysis using archaeal primers
... [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 JC8.0k
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Answer: A: How to reshape a fasta file?
... `perl -pe 's/\n// unless (/>/)' < FASTA > LINEARFASTA` ...
written 28 days ago by JC8.0k
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Answer: A: Filtering proteomics matrix before diff. exp.
... 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 JC8.0k
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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 JC8.0k
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Answer: A: How to remove a substring from each line with python 3
... Perl: `perl -pe 's/\[db_xref=Ensembl.+?\]//g' < input > output` ...
written 5 weeks ago by JC8.0k
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Comment: C: Recovering bam files after unknow deletion in the storage
... At some point, it could be cheaper just to sequence again the samples (if available) ...
written 5 weeks ago by JC8.0k

Latest awards to JC

Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Scholar 5 weeks ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Bioinformatician, Cellnetix Pathology And Laboratories, Seattle, Wa
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 5 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 7 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 8 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 12 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: What Should I Use Blat For?
Scholar 13 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome

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