User: atitparajuli2018

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Posts by atitparajuli2018

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Comment: C: Multiple Sequence Alignment using muscle
... Thank you for the suggestions. I will consider changing my strategy. ...
written 5 days ago by atitparajuli20180
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(Closed) Multiple Sequence Alignment using muscle
... I tried to align 112626 sequences of alfalfa using muscle command, but I get segmentation fault 11 error which is mainly due to low running memory. Then I split into 8 smaller files with 14100 sequences in each file. The muscle command ran smoothly in those files and generated output. However, when ...
multiple sequence alignment written 10 days ago by atitparajuli20180
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Comment: C: Multiple Sequence Alignment using muscle
... I have collected 320k ests from NCBI database, 47209 Ests from DDBJ and 54K Ests from Alfalfa Genome index (AGED). I am aligning these Ests together to generate a sequence which I will use as a reference sequence for Identifying the SNPs to the alfalfa lines that I have. I am working on identifying ...
written 24 days ago by atitparajuli20180
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Comment: C: Error characters in fasta file
... I did use the -seqtype nucleo option in the muscle command still I was getting the error message so I was asking for the code that does not give an error message as: I*** ERROR *** Invalid parameter -SeqType nucleo ...
written 24 days ago by atitparajuli20180
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Comment: C: Error characters in fasta file
... Please can you help me with the muscle command line for that? ...
written 24 days ago by atitparajuli20180
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Comment: C: Error characters in fasta file
... Yes it does. Can I clean these characters from the file? ...
written 24 days ago by atitparajuli20180
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Comment: C: Multiple Sequence Alignment using muscle
... I am preparing an exome capture library from these 112K ESTs. ...
written 24 days ago by atitparajuli20180
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Error characters in fasta file
... How do I remove invalid characters E, F, I, L, P, Q from a fasta file? I get these invalid characters while running *muscle* command for multiple sequence alignment. ...
fasta alignment muscle written 24 days ago by atitparajuli20180 • updated 23 days ago by zx87547.8k
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Multiple Sequence Alignment using muscle
... Hi, I keep getting an error segmentation fault 11 while running muscle command to align multiple sequences from a fasta file containing 112626 ESTs. Is it because of the large number of sequences that is causing the problem? I used the command $ ./muscle -in input.fa -out output.afa -maxite ...
alignment muscle written 24 days ago by atitparajuli20180 • updated 10 days ago by h.mon26k
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Comment: C: Express Sequence Tags information about Alfalfa
... The problem with ESTs using from few library ( I think) is, generally they are taken from the same sample (Treatment) and gene expression at that treatment, so If I use only that source to develop my library, then I think I will be missing other genes not expressed at the particular treatment. My re ...
written 9 weeks ago by atitparajuli20180

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