User: thomas.welch

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thomas.welch10
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t***********@ucdconnect.ie

Posts by thomas.welch

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Hisat2 aligner problem
... Hello there, I am currently having what appears to be the same issue with hisat2. the program hangs and give no stdout or stderr, but with an output .sam file that remains at 0 bytes without ever increasing in size no matter how long I wait. If you found a solution to this issue i'd be very gratef ...
written 5 months ago by thomas.welch10
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IGV indels not included in consensus sequence
... Hi there, I've been using the IGV to check quality of alignments of illumine sequences genomes, and to extract the consensus sequence for a particular gene of interest for population analysis. however when bringing the sequences together in mega I noticed that IGV had not included insertions in the ...
indels ngs alignment igv consensus sequence written 22 months ago by thomas.welch10 • updated 22 months ago by Biostar ♦♦ 20
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merging a number of overlapping sanger sequences
... Hi there, I have 80 DNA samples in which we have sequences three overlapping sections of a large gene using the sanger method. I am now looking for a way to merge these sequenced segments of the gene into a single sequence for each sample so that they can be aligned for analysis. I have come acros ...
sequence merge alignment written 2.2 years ago by thomas.welch10 • updated 14 months ago by ferroao20
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large deletion detection in a haploid microbial eukaryote
... Hi there, this is a very general question i'm afraid. but i've been searching for some time for a solution and can't find i concrete answer. I will soon have approximately 180 paired-end sequenced genome (x8-x13 coverage) of a haploid microbial genome, for which i am putting together a pipeline for ...
haploid microbial structural variant sequencing written 2.8 years ago by thomas.welch10 • updated 2.8 years ago by Brian Bushnell17k
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multiple sequence alignment for validation of large indels
... Hi there, I will soon have 180 illumina paired end sequenced genomes (approx 13x) with which i am conducting a GWAS experiment, these genomes are approximately 36Mbp long and have very long segmental indels (up 770kb). i intend to genotype my samples for these indels as a separate analysis from the ...
indels cnvnator multiple sequence alignment written 2.8 years ago by thomas.welch10
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Comment: C: blastall vs bl2seq, and blastall fasta output
... got it. this works perfectly. thank you very much. ...
written 3.1 years ago by thomas.welch10
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Comment: C: blastall vs bl2seq, and blastall fasta output
... thank you, but i don't think this will work either. the file for the organism i am investigating does not have chromosome coordinates (although there are of course query start and stop coordinates). it looks like i will have simply make a script to extract the correct (query) lines from the blastall ...
written 3.1 years ago by thomas.welch10
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Comment: C: blastall vs bl2seq, and blastall fasta output
... thank you for your help. however unfortunately this command does not give me the hit. the genome i have called formatdb on is a fasta file of shotgun sequence runs for a whole genome. while blastdbcmd gives me a fasta file of the accession which contains the hit, it does not give me the hit itself. ...
written 3.1 years ago by thomas.welch10
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blastall vs bl2seq, and blastall fasta output
... Hi there, I hope one of you guys can help me with this quite basic question. First of all i am trying to pick out homologs for phylogenetic analysis using standalone blast in the unix terminal. i am using a single gene in fasta format as query against a downloaded genome formatted with formatdb. I ...
fasta blastall bl2seq blast blast+ written 3.1 years ago by thomas.welch10

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Popular Question 22 months ago, created a question with more than 1,000 views. For merging a number of overlapping sanger sequences

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