User: ricfoz

gravatar for ricfoz
ricfoz30
Reputation:
30
Status:
New User
Location:
National School of Antropology and History, Mexico city, Mexico
Last seen:
4 months ago
Joined:
1 year, 7 months ago
Email:
r*****@hotmail.com

Posts by ricfoz

<prev • 61 results • page 1 of 7 • next >
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Comment: C: Trouble running Muscle on Mac OS
... Beauty of beauties, i have run my work with MAFFT, as you suggested. It ran neatly and fast. Thanks a lot for the suggestion of programs, and for everyone who run with this trouble, or question, i leave a paper that helped me, just as smoothly as Michael Dondrup's post: Sviatopolk-Mirsky Pais, de C ...
written 6 months ago by ricfoz30
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Comment: C: Trouble running Muscle on Mac OS
... Michael Donrup Thanks a lot for your answer, i have been reading about MAFFT and the other programs you suggest, i will give them a try. I am working with a dataset which i am not allowed to share plus, i am stubborn enough to try to get the job done with the resources i've got. Still, i am gratefu ...
written 6 months ago by ricfoz30
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Trouble running Muscle on Mac OS
... Hello community, I am trying to align a base with 22 sequences of a max length of 483656 base pairs, it is long, but not very, i am using a Sierra Mac OS, and i am using Muscle v3.8.31. I have used the following command line while standing where the program muscle is and where the base ...
toruble killed killed process muscle written 6 months ago by ricfoz30
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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 7 months ago by ricfoz30
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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 7 months ago by ricfoz30 • updated 7 months ago by Pierre Lindenbaum120k
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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 9 months ago by ricfoz30
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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 9 months ago by ricfoz30
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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 9 months ago by ricfoz30 • updated 9 months ago by RamRS22k
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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 12 months ago by ricfoz30
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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 12 months ago by ricfoz30

Latest awards to ricfoz

Popular Question 9 months ago, created a question with more than 1,000 views. For Editing headers from a vcf.gz file
Scholar 19 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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