ZhuHuangTianChi-hw1

GNBF5030 Homework 1

Student id: 1155228903

Question 1


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$ mkdir -p ~/5030/hw1/q1
$ cp /hdd1/shared/ecoli/sra_metadata/SraRunTable.txt ~/5030/hw1/q1/


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$ awk '{if($3 == "SINGLE") single++; if($3 == "PAIRED") paired++} END {print "Single-end: " single "\nPaired-end: " paired}' ~/5030/hw1/q1/SraRunTable.txt
Single-end: 35
Paired-end: 2

Answer: There are 35 Single-end samples and 2 Paired-end samples recorded in this table.


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$ awk 'NR > 1 && $6 > 300 {print $9}' ~/5030/hw1/q1/SraRunTable.txt | sort
SRR098026
SRR098028
SRR098031
SRR098033
SRR098040
SRR098041
SRR098043
SRR098044
SRR098279
SRR098280
SRR098281
SRR098282
SRR098283
SRR098284
SRR098286
SRR098287
SRR098288

Answer: SRR098026, SRR098028, SRR098031, SRR098033, SRR098040, SRR098041, SRR098043, SRR098044, SRR098279, SRR098280, SRR098281, SRR098282, SRR098283, SRR098284, SRR098286, SRR098287, SRR098288.


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$ grep -v '^BioSample_s' ~/5030/hw1/q1/SraRunTable.txt | awk '{if($4 ~ /^ZDB/) print $1}' | wc -l
30
$ grep -v '^BioSample_s' ~/5030/hw1/q1/SraRunTable.txt | awk '$4 !~ /<no/ {print substr($4, 1, 3)}' | sort | uniq
CZB
REL
ZDB

Answer: There are 30 sample names start with ZDB. And the other prefixes of sample names like ZDB are CZB, REL and ZDB.

Question 2


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$ mkdir -p ~/5030/hw1/q2
$ ln -s /hdd1/shared/bdgp6/data/rawdata/ ~/5030/hw1/q2/


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$ for file in ~/5030/hw1/q2/rawdata/*.fastq; do grep -c 'NNNNNN' "$file" | awk -v file="$file" '{print $1, file}' | awk -F'/' '{print $1, $NF}'; done | sort -rn > ~/5030/hw1/q2/consecutive_ns_count.txt

$ cat ~/5030/hw1/q2/consecutive_ns_count.txt
22049  SRR072915.fastq
20250  SRR072903.fastq
96  SRR072893.fastq
93  SRR072905.fastq

Answer: I think the dataset SRR072905.fastq have better quality based on the results above, because it contains less unknown nucleotides than other datasets.

Question 3


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$ mkdir -p ~/5030/hw1/q3
$ ln -s /hdd1/shared/bdgp6/data/genomes/BDGP6.Ensembl.93.gtf ~/5030/hw1/q3/BDGP6.Ensembl.93.gtf


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$ grep -v '^#' ~/5030/hw1/q3/BDGP6.Ensembl.93.gtf | awk '{print $3}' | sort | uniq -c
 160859 CDS
 187373 exon
  46299 five_prime_utr
  17737 gene
      4 Selenocysteine
  30492 start_codon
  33892 three_prime_utr
  34767 transcript

Answer: There are 8 annotations are associated with their feature type.


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$ grep -v '^#' ~/5030/hw1/q3/BDGP6.Ensembl.93.gtf | grep 'transcript' | awk '{print $10}' | cut -d ';' -f 1 | sed 's/"//g' | sort | uniq -c | sort -rn | head -10
   3896 FBgn0033159
   3830 FBgn0285944
   2208 FBgn0053196
   1682 FBgn0284408
   1354 FBgn0013733
   1180 FBgn0003429
   1018 FBgn0263111
    910 FBgn0263289
    900 FBgn0086906
    854 FBgn0085447


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$ awk '$3 == "gene" {print $1 "\t" $4 "\t" $5 "\t" $10}' ~/5030/hw1/q3/BDGP6.Ensembl.93.gtf | cut -d ';' -f 1 | sed 's/"//g' | awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" ($3-$2+1)}' > ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.bed

$ head ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.bed
3R      567076  2532932 FBgn0267431     1965857
3R      722370  722621  FBgn0085804     252
3R      1031171 1031354 FBgn0039987     184
3R      1366234 1366601 FBgn0267798     368
3R      1865108 1866008 FBgn0267797     901
3R      2156916 2157206 FBgn0058182     291
3R      2554162 3263582 FBgn0267430     709421
3R      2744304 2744800 FBgn0266747     497
3R      3322810 3354486 FBgn0086917     31677
3R      3461351 3587054 FBgn0010247     125704


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$ grep -v '^#' ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.bed | awk '{if($1 !~ /^211/) print $1}' | sort | uniq -c
   3496 2L
   3621 2R
   3457 3L
   4191 3R
    111 4
     38 mitochondrion_genome
     21 rDNA
      2 Unmapped_Scaffold_8
   2671 X
    113 Y

Answer: number of genes:

2L chromosome : 3496
2R chromosome: 3621
3L chromosome: 3457
3R chromosome: 4191
4 chromosome: 111
mitochondrion_genome chromosome: 38
rDNA chromosome: 21
Unmapped_Scaffold_8 chromosome: 2
X chromosome: 2671
Y chromosome: 113


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$ sort -k5,5nr ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.bed | head -n 50 > ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.longest50.bed && sort -k5,5nr ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.bed | tail -n 50 > ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.shortest50.bed

$ head ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.longest50.bed
3R      567076  2532932 FBgn0267431     1965857
3R      2554162 3263582 FBgn0267430     709421
3L      25236940        25670980        FBgn0267429     434041
2R      1866080 2262115 FBgn0263780     396036
X       2740384 3134532 FBgn0028369     394149
2R      326768  705848  FBgn0267428     379081
X       12043698        12335214        FBgn0267001     291517
3L      13521907        13803400        FBgn0264001     281494
Y       1636574 1884846 FBgn0046697     248273
X       7166451 7405797 FBgn0265457     239347
$ head ~/5030/hw1/q3/BDGP6.Ensembl.93.gene.shortest50.bed
3R      6451551 6451609 FBgn0283558     59
X       9236460 9236518 FBgn0263578     59
2R      14233130        14233187        FBgn0262427     58
3L      8354184 8354241 FBgn0263553     58
2R      10885533        10885589        FBgn0262412     57
2R      13852845        13852901        FBgn0283553     57
3R      24658605        24658660        FBgn0262431     56
2R      18180151        18180205        FBgn0286005     55
2R      19727098        19727152        FBgn0065076     55
3R      8308431 8308485 FBgn0263550     55

Question 4


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$ tar -czf /hdd1/5030-hw/Zhu_HuangTianChi\(5030-hw1\).tar.gz -C ~/5030 hw1


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$ chmod o-rwx /hdd1/5030-hw/Zhu_HuangTianChi\(5030-hw1\).tar.gz


$ du -sh ~/5030/hw1/
680K    /hdd1/home/f24_htczhu/5030/hw1/
$ df -h /hdd1
Filesystem      Size  Used Avail Use% Mounted on
/dev/sdc1        55T  3.3T   49T   7% /hdd1