User: Kevin D

gravatar for Kevin D
Kevin D10
Reputation:
10
Status:
New User
Location:
INRA France
Last seen:
2 years, 2 months ago
Joined:
2 years, 6 months ago
Email:
k***********@inra.fr

Posts by Kevin D

<prev • 14 results • page 1 of 2 • next >
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Find conserved blocks and extract subalignment with Python
... Hi everyone, After aligning DNA sequences, I would like to extract a sub alignment as follow: - scroll the alignment and find the first and last X-bp conserved blocks where X is a number given by the user. - extract the sub alignment surronded by the two conserved blocks. I tried this with pytho ...
conserved edges python multiple sequence alignment written 2.2 years ago by Kevin D10
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Comment: C: IUAPC codes in consensus sequence ? samtools mpileup / bcftools call / bcftools
... Yes, that is this option I mentionned I my post scriptum but when I turn it on, then all the variant positions appear heterozygous. In fact that is not true: I checked the mapping output and some variant are homozygous and others are heterozygous between reads, that is because they reflect two diffe ...
written 2.3 years ago by Kevin D10
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IUAPC codes in consensus sequence ? samtools mpileup / bcftools call / bcftools consensus
... Hello everyone! I mapped Forward and Reverse reads from one plant genome against a reference fasta sequence. As expected, there are varaints (SNP and indels). I am interested in retrieving the consensus sequence for downstream analysis. The reads come from a diploid plant genome and the gene of in ...
consensus bcftools iuapc written 2.3 years ago by Kevin D10 • updated 2.3 years ago by Pierre Lindenbaum121k
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What seems to work best to get consensus sequence after mapping: variant calling or de-novo assembly?
... Hi everyone! I have a question for the community and I wish I have your opinion and some piece of advise about it. I have a genomic sequence from a plant species on which I mapped Illumina paired reads (2*150 bp). Those reads come from another species from the same genus. Both species are closely-r ...
samtools mpileup bwa soap-denovo2 reads assembly written 2.4 years ago by Kevin D10
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Comment: C: Extracting pairwise alignment info
... Ok! Actually the "issue" is not of having the whole fraction. Let's say I have a second Emboss output file and the parameters are now: # Length: 1076 # Identity: 1062/1076 (98.7%) # Similarity: 1061/1076 (98.6%) # Gaps: 0/1076 ( 0.0%) # Score: 5248.0 Then the scri ...
written 2.4 years ago by Kevin D10
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Comment: C: Extracting pairwise alignment info
... Yes, I'll study them a lot, I guess I coud save so much time with them. Anyway, thanks for your coment, it's my first step toward bash script and it helped me understand the way it works! ...
written 2.4 years ago by Kevin D10
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Comment: C: Extracting pairwise alignment info
... Thank you, your solution is also nice because it takes the whole fraction "804/866" or "53/866" regardless of the number of digits. I mean, my final goal is to run the script on several Emboss output files and sometimes match numbers or gaps numbers have 2 or 3 or 4 digits so I guess jrj.healey's so ...
written 2.4 years ago by Kevin D10
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Comment: C: Extracting pairwise alignment info
... Thank you very much! It also works well! Now I see better how to use the grep function coupled with cut. Have a nice day! ...
written 2.4 years ago by Kevin D10
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Extracting pairwise alignment info
... Hello everyone, I am trying to write a bash script to extract information from a pairwise alignment text file output (Emboss Needle). In the txt output, there is a header as follow: #======================================= # # Aligned_sequences: 2 # 1: RC0505_OB1 # 2: RC050 ...
pairwise alignement grep sed unix awk written 2.4 years ago by Kevin D10 • updated 2.4 years ago by 5heikki8.4k
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Comment: C: Extracting a set of complete genes from de novo assembled unannotated contigs
... Right, I'm working on a diploid plant. I assume there are two copies because it is a 1st-generation interspecific hybrid so reads from either chromosome should not merge as the hybrid's parents are slightly different. I did not performed the assembly but I think Velvet was used to build contigs. I ...
written 2.5 years ago by Kevin D10

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