User: ricfoz

gravatar for ricfoz
ricfoz20
Reputation:
20
Status:
New User
Location:
National School of Antropology and History, Mexico city, Mexico
Last seen:
4 weeks ago
Joined:
1 year ago
Email:
r*****@hotmail.com

Posts by ricfoz

<prev • 58 results • page 1 of 6 • next >
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Comment: C: checking for cram to bam conversion syntax using samtools
... alright, the flag -T is used in order to build an index for the fasta file right?, just, in order to get the grip on the syntax, you write first the .bam file, and the .cram file next, since i am trying to convert cram to bam, wouldn't it have to be the other way around? ...
written 29 days ago by ricfoz20
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checking for cram to bam conversion syntax using samtools
... Hello everyone, I am trying to retreive some genic regions from a .cram file, i know the workflow starting with .bam files, so i want to convert some whole low coverage genomes from cram to bam I have been reading the manual and some how-to blogs, but i haven't come with a correct syntax to make t ...
syntax samtools cram to bam correct written 29 days ago by ricfoz20 • updated 29 days ago by Pierre Lindenbaum114k
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Comment: C: Error while trying to filter a .vcf.gz file with a bed.gz file
... Hello Ram, Well, i tried, it is a large file so it'll last, but it is generating the vcf file with the command you suggested. Thank yow for that awesomely fast answer. Best Regards R. ...
written 11 weeks ago by ricfoz20
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Comment: C: Error while trying to filter a .vcf.gz file with a bed.gz file
... Thanks a lot for the answer, i used the command call, since reading the manual it says that view is a former command, which on newer versions of bcftools (say 1-8 towards 1-9 versions) was changed to "call" , anyways, i will try, see what happens! R. ...
written 11 weeks ago by ricfoz20
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Error while trying to filter a .vcf.gz file with a bed.gz file
... Hello everyone, I am trying to filter a bgzipped vcf file with a bgzipped bed file. I have worked a script for that using bcftools-1.9 The script is: bcftools call -c -T bedfile.bed.gz chromosomefile.vcf.gz > filteredfile.vcf I get an error message which says: Wrong number of PL fiel ...
filter error bed file bed written 11 weeks ago by ricfoz20 • updated 11 weeks ago by RamRS19k
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How many works can clustalw can support at the same time?
... Hello everyone I am trying to align several fasta files using clustalw through a remote server in my university. The jobs are quite time consuming, and i am wondering if it is possible to run three jobs at the same time. I know i can, i just want to know if it is recommended, or if i just have to w ...
multiple jobs clustalw written 5 months ago by ricfoz20
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Comment: C: Issue while sorting a file
... .. I also ran the gdb command you suggested, it didn´t give any error message, it just worked as usually, outputting what the program is doing in a verbrose manner. but all ran smoothly. ...
written 5 months ago by ricfoz20
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Comment: C: Issue while sorting a file
... Thank you... I ran the pipe with wc -l as you suggested. The number of lines it tells the files have are the same !, i think that means that the info may be the same? It is very weird, still, i don't think there is any trouble with the compression with my samtools, since i have run the tool on othe ...
written 5 months ago by ricfoz20
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Issue while sorting a file
... hello everyone I am working with some bam files, and trying to retrieve a fasta sequence from them. I have sorted my workflow, but i have an inquiry since the size of the files doesn't seem to match, i describe my issue as follows: My original bam file has 2Gb size, when i sort it in order to ret ...
inconsistency trouble sort written 5 months ago by ricfoz20 • updated 5 months ago by drkennetz360
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looking for a tree viewer useful for .con.tre file outputted from MrBayes
... Hello community, I have run a Marcov Chain Monte Carlo analysis usin MrBayes. It run succesfuly and outputted (besides a few other files) a consensus .con.tre file which i was able to print in a tree viewer called FigTree-v1.4.3; it was pretty useful, but i have some branches which are short, and o ...
mrbayes viewer tree treeviewer written 6 months ago by ricfoz20 • updated 6 months ago by Kevin Blighe32k

Latest awards to ricfoz

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Editing headers from a vcf.gz file
Scholar 12 months ago, created an answer that has been accepted. For C: getting a consense one header .fasta file from a genic region, from .bam templat

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