User: xcalle91

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xcalle9120
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New User
Location:
European Union
Last seen:
3 years, 2 months ago
Joined:
4 years, 9 months ago
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Posts by xcalle91

<prev • 12 results • page 1 of 2 • next >
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Evaluated Structural consequences of single amino acid mutations
... Hi guys, I have a protein around 200 Aa ( which structure is known). I have 3 different sequences of the same protein with one point mutation in each case. I will like to evaluated in a computational way the effects of these alterations. I try to model it using homology modeling online tools ( su ...
sequence written 3.5 years ago by xcalle9120
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Answer: A: cutadapt does not keep sequences
... cutadapt -g ^GTAGATAGTGAA --discard-untrimmed A.fastq > E.fastq -g ^GTAGATAGTGAA: The adapter is expected to be a prefix of the read ...
written 3.8 years ago by xcalle9120
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Comment: C: cutadapt does not keep sequences
... thanks Jeremy! I found the solution ...
written 3.8 years ago by xcalle9120
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cutadapt does not keep sequences
... HI, I am trying to remove sequences that do not contain an adapter. the problem is that in the output I just can see the name of those reads but not the sequences. Example: A.fastq : @JZRAE:01332:11593 GTAGATAGTGAAAAAAAAAAAACCACAGCTTCCAAACACCATGACTCCATTATCACCGAGTCTGCCCAGGGGTAGAGAGGCTG ...
fastq sequencing written 3.8 years ago by xcalle9120
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(Closed) AA position to genomic location
... Hi! I have a big list of mutated amino acid positions, for each mutation I also have the related gene. I would like to end up with a bed file with all chromosome locations for each mutation. Given a position of an Amino acid, how can I get the chromosome location? Example: input: ...
genome written 4.1 years ago by xcalle9120
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aligner for intersection of chromosomic regions
... I have a list of 10 million elements ( each element is 2 base long) in a bed format. I also have a bed files with all the coding genes (each row been the start and ending points of the genes) I want to check how many elements fall into coding protein genes, an also see how many coding genes have b ...
alignment sequence written 4.2 years ago by xcalle9120
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Download multiple RNAseq experiments
... Hi! I would like to download many  human RNAseq raw data (up to 200, as many as I can). So far I have used  fastaq-dump + <RNAseq ID> but for doing this I have to find each one in pubmed (http://www.ncbi.nlm.nih.gov/sra/?term=). which is quite slow... Is it any place or anyway I can get th ...
rna-seq written 4.5 years ago by xcalle9120
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Comment: C: pysam duplicated sequence error
... Thanks Devon Ryan, that was the problem. I check the contigs and there were two duplicates. ...
written 4.5 years ago by xcalle9120 • updated 6 months ago by RamRS27k
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Comment: C: pysam duplicated sequence error
... thankss, Now It says: [samopen] SAM header is present: 1457 sequences. @SQ SN:NODE_4_length_21_cov_1.000000 LN:41 @SQ SN:NODE_4_length_21_cov_1.000000 LN:41 ...
written 4.5 years ago by xcalle9120 • updated 6 months ago by RamRS27k
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Comment: C: pysam duplicated sequence error
... It says: [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). ...
written 4.5 years ago by xcalle9120 • updated 6 months ago by RamRS27k

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For STAR aligner generating genomes takes long time

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