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  • Abhimanyu Singh
    106 days ago
    Questions (3)

    I mapped reads with
    bwa mem -M -t 40 allCombinedFinalSet.fa Seq.R1.fastq Seq.R2.fastq > aln.sam
    

    Extracted the mapped reads

    samtools view -f 0x2 -b aln.bam > output.bam
    

    Extracted the fastq

    bamToFastq -i output.bam -fq R1.fq -fq2 R2.fq 
    
    grep @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1 R1.fq             []
    @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
    @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
    @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
    

    I notice it has duplicated ....

    I think this because read was mapped twice (i.e. BWAmem).

    I tried fastuniq but it does not remove the duplicated reads.

    Can you please help me to remove duplicated reads from fastq files.

  • Bulbul
    107 days ago
    Questions (3)

    I wanted to remove the duplicates from fastq file. I planned to use fastuniq but it does not have good tutorial. Can you please tell me how to use it?

    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052249

  • Bulbul
    114 days ago
    Questions (1)

    Looking for files named in data ...Pushing back filename: "clean_a2017.R1.fq"
    Could not determine filetype from data 'clean_Avaga2017.R1.fq' ("clean_a2017.R1.fq")
    Pushing back filename: "clean_a2017.R2.fq"
    Could not determine filetype from data 'clean_a2017.R2.fq' ("clean_a2017.R2.fq")

    Fatal error (may be due to problems of the input data or parameters):

    ********************************************************************************
    * Some 'data' entries named in the manifest file could not be verified, see *
    * the log above. *
    * Maybe some files are missing, not readable or there is a typo in the *
    * manifest file? *
    ********************************************************************************

  • Marysia
    118 days ago
    Questions (2)

    I usually report and estimate the genome size by looking into file size of the contigs. Is this right way? 

  • Any
    166 days ago
    Questions (2)

    In school the teachers refer to both terms as one, but according to what I have read they are not the same and don't use the same methologies so I am a bit confused.

  • Marysia
    168 days ago
    Questions (1)

    I used the following command to print the blast hit.

    [Terminal] blastn -query aaa.fa -db blastdb/nt -evalue 10e-5 -num_threads 4 -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sallseqi sstart send evalue length frames qcovs' -out testBlastSee

    But the outfile print many hits, I only want the top one.

    [Terminal] more testBlastSee                                                                                                                  []
    Lactococcus_lactis    1    63350    1    63350    0.0    63350    1/1    100
    Lactococcus_lactis    52453    55105    138601    141250    0.0    2654    1/1    100
    Lactococcus_lactis    52393    53898    629230    627727    0.0    1508    1/1    100
    Lactococcus_lactis    52411    53898    2217595    2216111    0.0    1489    1/1    100
    Lactococcus_lactis    52413    53898    2157259    2155777    0.0    1487    1/1    100
    Lactococcus_lactis    52452    53898    838503    837059    0.0    1449    1/1    100
    Lactococcus_lactis    52453    53860    374322    375726    0.0    1409    1/1    100
    Lactococcus_lactis    53859    55105    2154570    2155816    0.0    1247    1/1    100
    Lactococcus_lactis    53860    55105    626521    627766    0.0    1246    1/1    100
    Lactococcus_lactis    53858    55105    835851    837098    0.0    1248    1/1    100
    Lactococcus_lactis    53860    55105    2214905    2216150    0.0    1246    1/1    100
    Lactococcus_lactis    53860    55104    374321    373077    0.0    1245    1/1    100
    Lactococcus_lactis    53860    55104    138600    137356    0.0    1245    1/1    100
    Lactococcus_lactis    53860    55104    839748    838504    0.0    1245    1/1    100
    Lactococcus_lactis    40213    41128    508317    507400    0.0    922    1/1    100
    Lactococcus_lactis    28448    28695    543445    543703    9e-96    260    1/1    100
    Lactococcus_lactis    42193    42376    506963    506780    4e-64    184    1/1    100
    Lactococcus_lactis    61964    62163    61646    61845    6e-53    200    1/1    100
    Lactococcus_lactis    61646    61845    61964    62163    6e-53    200    1/1    100
    Lactococcus_lactis    37541    37672    512963    512832    3e-50    132    1/1    100
    Lactococcus_lactis    28816    28933    2360018    2359903    7e-32    118    1/1    100
    Lactococcus_lactis    35284    35410    1439702    1439828    1e-30    129    1/1    100
    Lactococcus_lactis    28272    28363    1412439    1412348    1e-29    92    1/1    100
    Lactococcus_lactis    28193    28270    2360127    2360050    2e-28    78    1/1    100
    Lactococcus_lactis    28695    28813    542396    542514    6e-23    122    1/1    100
    Lactococcus_lactis    28695    28813    1981268    1981150    6e-23    122    1/1    100
    Lactococcus_lactis    28695    28813    2341071    2340953    6e-23    122    1/1    100
    Lactococcus_lactis    28695    28812    2360250    2360133    2e-22    121    1/1    100
    Lactococcus_lactis    28695    28796    2218330    2218229    8e-22    103    1/1    100
    Lactococcus_lactis    28695    28796    2260841    2260740    8e-22    103    1/1    100
    Lactococcus_lactis    55066    55147    2154609    2154528    2e-17    82    1/1    100
    Lactococcus_lactis    55066    55148    626559    626478    5e-14    83    1/1    100
    Lactococcus_lactis    52392    52456    373013    373076    2e-12    65    1/1    100
    Lactococcus_lactis    55105    55148    375723    375766    1e-09    44    1/1    100
    Lactococcus_lactis    52393    52457    839809    839745    1e-09    66    1/1    100

  • Anjana
    176 days ago
    Questions (0)

    When I tried Perl on my cluster/server it gives following error !! How to resolve it?

    $ perl
    perl: warning: Setting locale failed.
    perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_PAPER = "de_BE.UTF-8",
    LC_ADDRESS = "de_BE.UTF-8",
    LC_MONETARY = "de_BE.UTF-8",
    LC_NUMERIC = "de_BE.UTF-8",
    LC_TELEPHONE = "de_BE.UTF-8",
    LC_IDENTIFICATION = "de_BE.UTF-8",
    LC_MEASUREMENT = "de_BE.UTF-8",
    LC_TIME = "de_BE.UTF-8",
    LC_NAME = "de_BE.UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
    perl: warning: Falling back to a fallback locale ("en_US.UTF-8").

  • Shruti Paniwala
    178 days ago
    Questions (2)

    I am problem installing Perl module on cluster/server without root. Can you please recommend me a easy way or alternative way to install it.

  • Shruti Paniwala
    181 days ago
    Questions (1)

    I am looking for new, interactive and user friendly tools to see chromosomal rearrangements. I tried IGV, but it does not seems to be very helpful for chromosomal rearrangements visualization. Circos look pretty useless, as it does not allow me to explore well. Help Please...