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Search: Posts Made By: Manuelly
Forum: General 09-17-2019, 12:46 PM
Replies: 14
Views: 1,304
Posted By Manuelly
I think I did not express myself well. I need a...

I think I did not express myself well. I need a single fasta per sample and not interleaved. like that:
>1 NC_012920.1:1-16569
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT...
Forum: General 09-17-2019, 11:50 AM
Replies: 14
Views: 1,304
Posted By Manuelly
1.after extracting the consensus in fasta format,...

1.after extracting the consensus in fasta format, I opened fasta and came across this:
>E00382:156:HMFJCCCXX:1:1102:7659:38315/2...
Forum: General 09-17-2019, 10:39 AM
Replies: 14
Views: 1,304
Posted By Manuelly
thank you very much for all the help. I realize...

thank you very much for all the help. I realize that I have difficulty understanding the syntax of some commands and I don't know how to overcome this difficulty. Like "for i in *.bam". Is there any...
Forum: General 09-12-2019, 05:48 AM
Replies: 14
Views: 1,304
Posted By Manuelly
1.I opened the directory with the files in the...

1.I opened the directory with the files in the terminal.
2. Then I used the following command:
reformat.sh in=${i}.bam out=${i}.fa
3. I received the following message:
java -ea -Xms300m -cp...
Forum: General 09-11-2019, 07:44 AM
Replies: 14
Views: 1,304
Posted By Manuelly
I tried to execute the command and the following...

I tried to execute the command and the following message appeared. Do you know how I can solve this?
/media/lucasmalzoni/Seagate Backup Plus Drive1/Joao/MT/02-Bam$ reformat.sh in=${i}.bam...
Forum: General 08-28-2019, 07:11 AM
Replies: 14
Views: 1,304
Posted By Manuelly
so using reformat.sh command can I convert...

so using reformat.sh command can I convert multiple bam to fasta at once? for this i need to open the folder with all bam and run the command?
Sorry, if the question is too obvious, but I'm still...
Forum: General 08-27-2019, 11:31 AM
Replies: 14
Views: 1,304
Posted By Manuelly
how convert several bam files to fasta?

Hello!
I have 1979 mtDNA bam files and I need to convert these files to individual fastas. Since there are so many files, I would like to do this conversion faster or even once. I have no idea how...
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