User: jaqx008
jaqx008 • 30
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Posts by jaqx008
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... Thanks. My organism (lancelet) does not have a well anotated genome. I did blast the 21nt sequence and got a protein that I assume should correspond to were the siRNA regulate. I used this protein to blast a related specie (Homo sapien or mouse). and got
BCAT_beta_family cd01557
BCAT_beta ...
written 2 days ago by
jaqx008 • 30
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... Hello Guys, This is not much of a computation question. I made this count table bar graphs for siRNA I have from RNAseq data of a female organism. overral, the siRNA was low for all BUT ONE loci. Im trying to identify the mRNA regulated by this one siRNA (ACCCATAGATCCGAGCTTGTG) but dont know how to ...
written 3 days ago by
jaqx008 • 30
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Answer:
A: GREP: out of memory
... I was able to resolve this issue. If anyone else runs into the same problem, the command bellow should help.
first split files into few lines using
split -l n file.txt
where n= number of lines desired (I did n = 5)
$ for i in x*; do grep -f "$i" file2.gff > "$i".tmp.gff; done &&am ...
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Comment:
C: GREP: out of memory
... Yes I am trying to pull out certain genes IDs with there corresponding information. I posted in the comment above what my files look like. the thing is, it works fine for some and does not for others. ...
written 13 days ago by
jaqx008 • 30
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Comment:
C: GREP: out of memory
... Hey, Where in the command would you put -m? I mean where in
while read line; do grep -wF "$line" 2.gff; done < 1.txt ...
written 13 days ago by
jaqx008 • 30
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Comment:
C: GREP: out of memory
... OK. the text files rang between 100bytes to about 50kb with word count around 1500 and in this format
2597857964
2597857966
2597857965
2597857963
2597860200
2597857153
2597857472
while the .gff range from about 600kb to about 900kb with wc of about 5000 to 7000 in the f ...
written 13 days ago by
jaqx008 • 30
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Comment:
C: GREP: out of memory
... This is what I am trying to do. there are some gene IDs in a text file A, and lines possibly containing the gene IDs in gff file B. I am trying to identify the matches in B and outpur all the lines that match in B ( this should output all the columns in B.
A has only one column of gene IDs
B has has ...
written 13 days ago by
jaqx008 • 30
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Comment:
C: GREP: out of memory
... well I cant post more than 5 times in 6 hours and thats why I havent responded. BTW I am grep-ing a text file like
2345
3245
5432
1234
against a .gff file like
4634 - ID=2345
4353 + ID=3245
etc
its working for some and giving memory complain for others. ...
written 13 days ago by
jaqx008 • 30
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Comment:
C: GREP: out of memory
... I did this and it worked for one of the txt already but one gave this error. does it mean no match?
grep: empty (sub)expression ...
written 14 days ago by
jaqx008 • 30
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Comment:
C: GREP: out of memory
... It gives a long list that looks like this then terminates aftyer I run the command
grep: illegal byte sequence
grep: illegal byte sequence
grep: illegal byte sequence
grep: illegal byte sequence
grep: output.txt: No such file or directory
grep: illegal byte sequence
grep ...
written 14 days ago by
jaqx008 • 30
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