User: amy_houseman
amy_houseman • 0
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Posts by amy_houseman
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... Hi,
So after installing samtools and doing the above command, I get [this result:][1]
![samtools view][2]
I haven't changed the .sam to a .bam file yet, so I'll await your response till I do so.
Thanks for all your help.
Amy
[1]: https://1drv.ms/u/s!ArwhyLzdnOxrguh4sLOe8fi4y-tDsg?e=J1Azvv
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written 19 days ago by
amy_houseman • 0
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... Hi!
The result of file my_results.sam is this: (which also doesn't look very promising): `my_results.sam: Blocked GNU Zip Format (BGZF; gzip compatible), block length 246`
Thanks again
...
written 20 days ago by
amy_houseman • 0
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... Hi all,
I have DNA Sanger sequence FASTA files from patient TGM1 genes, and have been trying to use subread to align them to the TGM1 coding reference sequence from [NCBI][1].
I keep getting a weird red looking .sam file as the result from the alignment but it doesn't look correct at all. I've a ...
written 20 days ago by
amy_houseman • 0
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... I have some DNA nucleotide sequences from exons in TGM1 gene of people with disease, so I'm trying to align them to the reference coding sequence of TGM1, and then hopefully find the variants and then use another tool after to find the pathogenicity of each variant? If that makes sense.
Do you kno ...
written 20 days ago by
amy_houseman • 0
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... Hi,
I made that change but it still doesn't seem to work, the command does seem to create 5 file types but they end up in the `fasta_reference_TGM1_folder`.
If I manually move these files into the `TGM1_index` file and then run:
`subread-align -T 1 -i /home/amyhouseman/Desktop/fasta_reference_T ...
written 20 days ago by
amy_houseman • 0
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... Hi!
The return for that is:
-rw-rw-r-- 1 amyhouseman amyhouseman 0 Feb 9 12:51 /home/amyhouseman/Desktop/fasta_reference_TGM1_folder/TGM1_index
The process I did to get to this point was:
> 1. Installed subread from the website: http://bioinf.wehi.edu.au/subread-package/
> 2. sudo apt ...
written 21 days ago by
amy_houseman • 0
• updated
21 days ago by
GenoMax ♦ 96k
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... Its around 2,453bp (its the coding seq for https://www.ncbi.nlm.nih.gov/nuccore/NM_000359.3).
I think my laptop may only be 8GB of RAM as I think its this one: https://www.laptopsdirect.co.uk/lenovo-v15-ada-amd-ryzen-3-3250u-8gb-256gb-ssd-15.6-inch-fhd-windows-10-lap-82c70004uk/version.asp
Sorry ...
written 22 days ago by
amy_houseman • 0
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... Hi, I'm not sure, when I go to settings it says: Memory 5.7GiB.. Disk capacity 256.1GB. Although, I did dual boot the laptop so it has both windows and Ubuntu. So that might not be helping? Thanks! ...
written 22 days ago by
amy_houseman • 0
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... ah yes! Such a simple error, thank you!
However, now it says 'Segmentation fault (core dumped)' - which I assume is a memory error? But I checked the system monitor and I'm only using 20% - Thanks for your help, I really appreciate it ...
written 22 days ago by
amy_houseman • 0
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... Hi, thanks for your reply. I meant this is the code I entered (please excuse my messy files):
subread-align -i home/amyhouseman/Desktop/fasta_reference_TGM1_folder/TGM1_index -r /home/amyhouseman/Desktop/katja_fasta_seq/fasta_trimmed_sequences/fasta_trimmed_1_all/fasta_trimmed_1_final -t 1 -o ...
written 22 days ago by
amy_houseman • 0
• updated
22 days ago by
GenoMax ♦ 96k
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