User: atitparajuli2018

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Posts by atitparajuli2018

<prev • 14 results • page 1 of 2 • next >
5
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Separate output file for cluster from cd-hit-est
... Is there any option in cd-hit-est to give separate output files for each of different clusters? ...
alignment written 7 months ago by atitparajuli20180 • updated 7 months ago by Joe16k
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(Closed) Extracting sequence less than N length from FASTA file
... How do I extract sequences less than 800 bp from a fasta file, I used the following command to extract but I was not successful in doing so. I still have some sequences more than 800 bp in length. command: $ awk 'BEGIN {RS = ">" ; ORS = ""} length ($2) <= 800 {print ">"$0}' input.fasta > ...
sequence written 7 months ago by atitparajuli20180
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324
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Comment: C: Multiple Sequence Alignment using muscle
... Thank you for the suggestions. I will consider changing my strategy. ...
written 8 months 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 8 months 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 9 months 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 9 months 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 9 months 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 9 months 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 9 months ago by atitparajuli20180
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6 follow
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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 9 months ago by atitparajuli20180 • updated 9 months ago by zx87549.1k

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