User: wes

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wes40
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Posts by wes

<prev • 22 results • page 1 of 3 • next >
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Plastome related question
... Anyone has the experience of using GeSeq? Please advise how to extract the information on number of protein-coding genes number and tRNA genes? I found out that number of tRNAs shown at the tRNAscan-SE v2.0.7 (number=36) button is different from tRNAscan-SE_v2 (number=35) found in GFF3. Any idea why ...
sequence written 2 days ago by wes40
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Comment: C: How to view the sequence of the transparently mapped reads
... yes, thanks for the guidance and it works! ...
written 10 days ago by wes40
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How to view the sequence of the transparently mapped reads
... I would like to map the Illumina reads against the assembled genome. There is two regions in the genome with inverted repeat. Therefore, it is expected to observe alignment with transparent border in IGV. According to the link below, it stated that alignments that are displayed with light gray borde ...
alignment written 10 days ago by wes40 • updated 10 days ago by GenoMax94k
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IGV related questions
... 1. May I know what is the triangle icon (between coverage and track file) in the IGV represent? ![enter image description here][1] 2. May I know what is the count below means? From my understanding, for that particular base position, there is 222 reads with G aligned to the reference at that partic ...
alignment written 12 days ago by wes40 • updated 12 days ago by Pierre Lindenbaum133k
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Mapping reads to circular references
... Is there any program can be used to map subreads (from pacbio) against circular references (plastome)? Previously, I tried to use minimap to map against the reference. However, there is a drop in coverage at both ends of the reference. ...
alignment written 25 days ago by wes40
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how to determine number of subreads that spanned across certain region
... May I know how to determine the number of subreads that span a certain region besides counting the subreads manually using the IGV? ...
alignment written 27 days ago by wes40 • updated 27 days ago by Alex Reynolds31k
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Searching subreads used to assemble contig of interest (canu)
... I use canu to assemble pacbio data. From the contigs.layout.readToTig file, I can find the reads that are used to assemble a particular contig. However, the read ID does not match the original subreads ID. Is there any way to relate the read ID found in contigs.layout.readToTig file to the original ...
assembly written 5 weeks ago by wes40
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Organelle annotation using GeSeq
... Anyone has the experience perform organelle annotation using GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html)? May I know how to determine number of 1) protein-coding genes, 2) tRNAs and 3) rRNAs? Which tool should I get the information from the GFF3? blatN? blatX? HMMER? Chloe? or tRNAscan-S ...
assembly written 6 weeks ago by wes40
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Minia assembler _ header information
... Minia assembler had been used for assembly. From the output file, header of one of the contigs is showed below. May I know where can I find the coverage information for the contig with the name "10". In addition, what is the other abbreviation means? >10 LN:i:562 KC:i:5029 km:f:9.635 L:+:2237 ...
assembly written 8 weeks ago by wes40
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Comment: C: Align pacbio subreads against assembled pacbio reads
... Thanks for the recommendation! ...
written 8 weeks ago by wes40

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