User: harold.smith.tarheel

Reputation:
4,030
Status:
Trusted
Location:
United States
Last seen:
26 minutes ago
Joined:
2 years, 8 months ago
Email:
h*******************@gmail.com

Posts by harold.smith.tarheel

<prev • 486 results • page 1 of 49 • next >
0
votes
1
answer
116
views
1
answers
Comment: C: look for sequences containing a specific motif
... From the user guide: > You can specify whether or not BBDuk looks for the reverse-complement > of the reference sequences as well as the forward sequence with the > flag “rcomp=t” or “rcomp=f”; by default it looks for both. ...
written 10 days ago by harold.smith.tarheel4.0k
4
votes
1
answer
116
views
1
answers
Answer: A: look for sequences containing a specific motif
... An easy method would be to use [BBMap][1]'s kmer counting functionality, plus hamming distance to allow for errors: bbduk.sh in=YOUR.FASTQ outm=MATCHED.FASTQ \ literal=SEARCH_STRING k=STRING_LENGTH hdist=NUMBER_OF_ERRORS [1]: https://sourceforge.net/projects/bbmap/ ...
written 11 days ago by harold.smith.tarheel4.0k
0
votes
2
answers
137
views
2
answers
Answer: A: Gene distribution along the chromosomes
... This [post][1] shows how to bin feature counts by chromosome intervals (substitute gene position file for VCF). Then use R (or even the dreaded Excel) to generate the plot. [1]: https://www.biostars.org/p/218480/ ...
written 11 days ago by harold.smith.tarheel4.0k
0
votes
4
answers
385
views
4
answers
Answer: A: A very short gene with very high TPM
... The only short sequence string that's likely to present in 60% of reads is the adapter. ...
written 26 days ago by harold.smith.tarheel4.0k
0
votes
0
answers
29
views
0
answers
Comment: C: Bioinformaticist or bioinformatician?
... Apologies - didn't pop up in the search function. Will delete. ...
written 5 weeks ago by harold.smith.tarheel4.0k
2
votes
2
answers
198
views
2
answers
Answer: A: vcf files: counting number of variants in genomic windows of chosen size
... See https://www.biostars.org/p/218480/ ...
written 9 weeks ago by harold.smith.tarheel4.0k
1
vote
3
answers
320
views
3
answers
Comment: C: SNP Analysis of bacterial genomes
... Are you attempting to determine whether the two strains are identical, or the mechanism of antibiotic resistance? If the latter, be aware that resistance typically arises from acquisition of a resistance cassette (often transmitted via plasmid) rather than mutation. SNP analysis would not identify a ...
written 9 weeks ago by harold.smith.tarheel4.0k
2
votes
2
answers
294
views
2
answers
Answer: C: Bedtools intersect returns 0, intersections present on IGV
... It looks like your chromosome notation is NOT identical. Your IGV screenshot says 'chr6' but your gene.ROI says 'Chr6'. Linux is case-sensitive. ...
written 10 weeks ago by harold.smith.tarheel4.0k
0
votes
1
answer
272
views
1
answers
Comment: C: Can phasing or pre-phase during basecall cause indel?
... @Kevin Blighe, the error rate is distinct from phasing issues. It's determined by aligning the phiX spike-in to the reference and calculating the percentage of differences between the two. The majority of those errors are single nucleotide mismatches, which can be caused by PCR misincorporation erro ...
written 10 weeks ago by harold.smith.tarheel4.0k
2
votes
1
answer
272
views
1
answers
Comment: C: Can phasing or pre-phase during basecall cause indel?
... PCR-generated indels are a known problem (at least for most bench scientists) - it's why Illumina developed a PCR-free library prep. They're most common in homopolymers runs (mono/di/trinucleotide repeats). As @d-cameron noted, indels introduced during library prep will be homogeneous in the cluste ...
written 10 weeks ago by harold.smith.tarheel4.0k

Latest awards to harold.smith.tarheel

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 10 days ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 9 weeks ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For C: Illumina Instrument Type from fastq?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 5 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Scholar 6 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 6 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 8 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 8 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 8 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Scholar 9 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Scholar 13 months ago, created an answer that has been accepted. For A: Where to Download & File Format of Reference Gene Annotation for C. elegans WS22
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Per base sequence quality before and after truseq adapters removal
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Can Q10 be better than Q30

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 663 users visited in the last hour